Starting phenix.real_space_refine on Wed Sep 17 03:17:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cu8_7619/09_2025/6cu8_7619.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cu8_7619/09_2025/6cu8_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 { model { file = "/net/cci-nas-00/data/ceres_data/6cu8_7619/09_2025/6cu8_7619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cu8_7619/09_2025/6cu8_7619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cu8_7619/09_2025/6cu8_7619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cu8_7619/09_2025/6cu8_7619.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2880 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" 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: A, B, C, D, F, G, H, I, J Time building chain proxies: 0.40, per 1000 atoms: 0.14 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: 0.19 Conformation dependent library (CDL) restraints added in 83.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.11 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: 0.24 Time building geometry restraints manager: 0.28 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: 0.01 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' 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: 0.430 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.000 ------------------------------------------------------------------------------- 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= 0.173 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 2880) covalent geometry : angle 0.72590 ( 3900) hydrogen bonds : bond 0.21820 ( 13) hydrogen bonds : angle 8.12127 ( 39) *********************** 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 to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.065 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: 0.0469 time to fit residues: 6.5589 Evaluate side-chains 69 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 40.0000 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 40.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 40.0000 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN D 79 GLN H 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.113855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.100266 restraints weight = 7249.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.102366 restraints weight = 3644.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.103765 restraints weight = 2342.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.104718 restraints weight = 1748.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.105436 restraints weight = 1426.798| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2880 Z= 0.194 Angle : 0.745 4.118 3900 Z= 0.444 Chirality : 0.055 0.123 540 Planarity : 0.003 0.012 480 Dihedral : 7.217 16.037 400 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.26 % Allowed : 11.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.41), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 2880) covalent geometry : angle 0.74488 ( 3900) hydrogen bonds : bond 0.04263 ( 13) hydrogen bonds : angle 6.34598 ( 39) *********************** 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 72 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.133 Fit side-chains REVERT: E 61 GLU cc_start: 0.7349 (pm20) cc_final: 0.7054 (pm20) REVERT: A 58 LYS cc_start: 0.8693 (mttp) cc_final: 0.7488 (pttm) REVERT: A 61 GLU cc_start: 0.7704 (pm20) cc_final: 0.6086 (mm-30) REVERT: B 61 GLU cc_start: 0.8081 (pt0) cc_final: 0.6350 (tp30) REVERT: G 61 GLU cc_start: 0.7273 (pm20) cc_final: 0.7003 (pm20) REVERT: G 62 GLN cc_start: 0.6910 (mt0) cc_final: 0.6704 (mt0) REVERT: H 61 GLU cc_start: 0.7355 (pm20) cc_final: 0.7104 (pm20) outliers start: 7 outliers final: 3 residues processed: 71 average time/residue: 0.0393 time to fit residues: 3.8097 Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.073 ------------------------------------------------------------------------------- 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 16 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.116385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.102700 restraints weight = 7285.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.105026 restraints weight = 3620.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.106549 restraints weight = 2296.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.107485 restraints weight = 1683.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.108281 restraints weight = 1380.823| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4234 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= 0.177 Angle : 0.677 3.782 3900 Z= 0.405 Chirality : 0.055 0.123 540 Planarity : 0.003 0.013 480 Dihedral : 6.923 15.473 400 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.87 % Allowed : 13.23 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (0.39), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 2880) covalent geometry : angle 0.67738 ( 3900) hydrogen bonds : bond 0.04059 ( 13) hydrogen bonds : angle 5.64538 ( 39) *********************** 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 68 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.110 Fit side-chains REVERT: E 79 GLN cc_start: 0.9052 (tt0) cc_final: 0.8583 (tt0) REVERT: A 61 GLU cc_start: 0.7976 (pm20) cc_final: 0.6050 (mm-30) REVERT: B 61 GLU cc_start: 0.7943 (pt0) cc_final: 0.6190 (mm-30) REVERT: G 61 GLU cc_start: 0.7679 (pm20) cc_final: 0.7349 (pm20) REVERT: H 61 GLU cc_start: 0.7201 (pm20) cc_final: 0.6924 (pm20) REVERT: I 61 GLU cc_start: 0.7217 (pm20) cc_final: 0.6986 (pm20) REVERT: J 61 GLU cc_start: 0.7399 (pm20) cc_final: 0.6979 (pm20) outliers start: 12 outliers final: 7 residues processed: 67 average time/residue: 0.0356 time to fit residues: 3.2605 Evaluate side-chains 53 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.094 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 3 optimal weight: 40.0000 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 28 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 30.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.124520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.111283 restraints weight = 6730.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.113750 restraints weight = 3159.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.115414 restraints weight = 1941.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.116355 restraints weight = 1392.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.117368 restraints weight = 1139.705| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2880 Z= 0.089 Angle : 0.560 4.178 3900 Z= 0.329 Chirality : 0.053 0.122 540 Planarity : 0.002 0.012 480 Dihedral : 5.850 13.118 400 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.97 % Allowed : 17.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.44), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00171 ( 2880) covalent geometry : angle 0.55964 ( 3900) hydrogen bonds : bond 0.03047 ( 13) hydrogen bonds : angle 5.01360 ( 39) *********************** 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 60 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.111 Fit side-chains REVERT: A 61 GLU cc_start: 0.8060 (pm20) cc_final: 0.6083 (mm-30) REVERT: A 75 THR cc_start: 0.7539 (m) cc_final: 0.6923 (p) REVERT: B 61 GLU cc_start: 0.7839 (pt0) cc_final: 0.6116 (mm-30) REVERT: G 61 GLU cc_start: 0.7857 (pm20) cc_final: 0.7607 (pm20) REVERT: H 75 THR cc_start: 0.8255 (m) cc_final: 0.7646 (p) REVERT: I 61 GLU cc_start: 0.6989 (pm20) cc_final: 0.6553 (pm20) outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 0.0253 time to fit residues: 2.2844 Evaluate side-chains 56 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain D 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 8 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 overall best weight: 5.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.119006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.105166 restraints weight = 7051.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.107587 restraints weight = 3527.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.109243 restraints weight = 2217.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.110317 restraints weight = 1610.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.111125 restraints weight = 1290.546| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2880 Z= 0.156 Angle : 0.612 3.571 3900 Z= 0.363 Chirality : 0.054 0.126 540 Planarity : 0.003 0.013 480 Dihedral : 6.196 14.040 400 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.90 % Allowed : 17.74 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.43), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2880) covalent geometry : angle 0.61231 ( 3900) hydrogen bonds : bond 0.03466 ( 13) hydrogen bonds : angle 5.48283 ( 39) *********************** 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 61 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.113 Fit side-chains REVERT: A 61 GLU cc_start: 0.8155 (pm20) cc_final: 0.6114 (mm-30) REVERT: B 61 GLU cc_start: 0.7954 (pt0) cc_final: 0.6229 (mm-30) outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.0332 time to fit residues: 2.9099 Evaluate side-chains 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 75 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 25 optimal weight: 8.9990 chunk 28 optimal weight: 40.0000 chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 30.0000 chunk 20 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 27 optimal weight: 30.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.114901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.101367 restraints weight = 7380.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.103647 restraints weight = 3801.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.105191 restraints weight = 2427.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.106204 restraints weight = 1777.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.106940 restraints weight = 1433.403| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2880 Z= 0.228 Angle : 0.705 4.031 3900 Z= 0.419 Chirality : 0.057 0.130 540 Planarity : 0.003 0.013 480 Dihedral : 6.987 15.936 400 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 4.52 % Allowed : 16.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.80 (0.38), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 2880) covalent geometry : angle 0.70524 ( 3900) hydrogen bonds : bond 0.04119 ( 13) hydrogen bonds : angle 5.57966 ( 39) *********************** 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 62 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.118 Fit side-chains REVERT: A 61 GLU cc_start: 0.8326 (pm20) cc_final: 0.6159 (mm-30) REVERT: B 57 GLU cc_start: 0.3289 (OUTLIER) cc_final: 0.2489 (pt0) REVERT: B 61 GLU cc_start: 0.8076 (pt0) cc_final: 0.6301 (mm-30) REVERT: F 62 GLN cc_start: 0.7272 (mt0) cc_final: 0.6770 (mp10) REVERT: G 61 GLU cc_start: 0.8048 (pm20) cc_final: 0.7752 (pm20) outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 0.0351 time to fit residues: 2.9043 Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 0.0670 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 overall best weight: 5.6124 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.117687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.103812 restraints weight = 7060.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.106227 restraints weight = 3593.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.107829 restraints weight = 2288.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.109015 restraints weight = 1669.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.109581 restraints weight = 1325.113| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2880 Z= 0.160 Angle : 0.619 3.661 3900 Z= 0.366 Chirality : 0.055 0.128 540 Planarity : 0.003 0.013 480 Dihedral : 6.496 14.668 400 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 4.19 % Allowed : 18.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.38), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2880) covalent geometry : angle 0.61943 ( 3900) hydrogen bonds : bond 0.03794 ( 13) hydrogen bonds : angle 5.40661 ( 39) *********************** 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 to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.147 Fit side-chains REVERT: A 61 GLU cc_start: 0.8291 (pm20) cc_final: 0.6127 (mm-30) REVERT: B 57 GLU cc_start: 0.3214 (OUTLIER) cc_final: 0.2585 (pt0) REVERT: B 61 GLU cc_start: 0.7909 (pt0) cc_final: 0.6219 (mm-30) REVERT: F 62 GLN cc_start: 0.7293 (mt0) cc_final: 0.6805 (mp10) REVERT: G 61 GLU cc_start: 0.8015 (pm20) cc_final: 0.7735 (pm20) outliers start: 13 outliers final: 8 residues processed: 56 average time/residue: 0.0386 time to fit residues: 2.9643 Evaluate side-chains 53 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 30.0000 chunk 31 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.116858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.102971 restraints weight = 7302.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.105385 restraints weight = 3700.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.106991 restraints weight = 2327.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.108096 restraints weight = 1683.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.108830 restraints weight = 1345.865| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2880 Z= 0.167 Angle : 0.636 4.516 3900 Z= 0.374 Chirality : 0.056 0.128 540 Planarity : 0.003 0.015 480 Dihedral : 6.473 14.751 400 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.52 % Allowed : 18.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.79 (0.38), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 2880) covalent geometry : angle 0.63557 ( 3900) hydrogen bonds : bond 0.03759 ( 13) hydrogen bonds : angle 5.41623 ( 39) *********************** 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 58 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.117 Fit side-chains REVERT: A 61 GLU cc_start: 0.8279 (pm20) cc_final: 0.6139 (mm-30) REVERT: B 57 GLU cc_start: 0.3424 (OUTLIER) cc_final: 0.2749 (pt0) REVERT: B 61 GLU cc_start: 0.7996 (pt0) cc_final: 0.6238 (mm-30) REVERT: F 62 GLN cc_start: 0.7300 (mt0) cc_final: 0.6806 (mp10) REVERT: G 61 GLU cc_start: 0.8029 (pm20) cc_final: 0.7687 (pm20) outliers start: 14 outliers final: 10 residues processed: 55 average time/residue: 0.0368 time to fit residues: 2.8192 Evaluate side-chains 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 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 25 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.111679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.098203 restraints weight = 7616.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.100406 restraints weight = 3974.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.101869 restraints weight = 2556.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.102855 restraints weight = 1875.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.103609 restraints weight = 1506.039| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2880 Z= 0.295 Angle : 0.772 4.900 3900 Z= 0.458 Chirality : 0.059 0.135 540 Planarity : 0.004 0.019 480 Dihedral : 7.548 16.920 400 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.44 % Favored : 82.56 % Rotamer: Outliers : 4.52 % Allowed : 18.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.65 (0.33), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.25), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00626 ( 2880) covalent geometry : angle 0.77234 ( 3900) hydrogen bonds : bond 0.04512 ( 13) hydrogen bonds : angle 5.67866 ( 39) *********************** 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 61 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.115 Fit side-chains REVERT: E 79 GLN cc_start: 0.9034 (tt0) cc_final: 0.8669 (tt0) REVERT: A 57 GLU cc_start: 0.3697 (OUTLIER) cc_final: 0.2313 (pm20) REVERT: A 61 GLU cc_start: 0.8322 (pm20) cc_final: 0.6100 (mm-30) REVERT: A 79 GLN cc_start: 0.8953 (tt0) cc_final: 0.8511 (tt0) REVERT: B 57 GLU cc_start: 0.3773 (OUTLIER) cc_final: 0.2919 (pt0) REVERT: B 61 GLU cc_start: 0.8164 (pt0) cc_final: 0.6600 (tp30) REVERT: F 62 GLN cc_start: 0.7459 (mt0) cc_final: 0.6872 (mp10) outliers start: 14 outliers final: 10 residues processed: 57 average time/residue: 0.0290 time to fit residues: 2.4220 Evaluate side-chains 58 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 27 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.119874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.106104 restraints weight = 7115.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.108664 restraints weight = 3429.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.110435 restraints weight = 2108.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.111488 restraints weight = 1509.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.112423 restraints weight = 1212.391| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2880 Z= 0.121 Angle : 0.615 5.373 3900 Z= 0.358 Chirality : 0.055 0.132 540 Planarity : 0.002 0.015 480 Dihedral : 6.365 14.540 400 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 2.58 % Allowed : 19.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.37), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 2880) covalent geometry : angle 0.61536 ( 3900) hydrogen bonds : bond 0.03411 ( 13) hydrogen bonds : angle 5.29282 ( 39) ********************** 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 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.117 Fit side-chains REVERT: A 61 GLU cc_start: 0.8297 (pm20) cc_final: 0.6106 (mm-30) REVERT: B 57 GLU cc_start: 0.3187 (OUTLIER) cc_final: 0.2564 (pt0) REVERT: B 61 GLU cc_start: 0.7940 (pt0) cc_final: 0.6324 (mm-30) REVERT: F 62 GLN cc_start: 0.7507 (mt0) cc_final: 0.7036 (mp10) REVERT: G 61 GLU cc_start: 0.7846 (pm20) cc_final: 0.7538 (pm20) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.0300 time to fit residues: 2.2749 Evaluate side-chains 52 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 J residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 40.0000 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 37 optimal weight: 0.2980 chunk 19 optimal weight: 0.4980 chunk 35 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.119823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.105814 restraints weight = 7042.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.108378 restraints weight = 3454.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.110143 restraints weight = 2138.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.111356 restraints weight = 1534.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.112163 restraints weight = 1207.551| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2880 Z= 0.133 Angle : 0.594 4.838 3900 Z= 0.348 Chirality : 0.054 0.127 540 Planarity : 0.003 0.017 480 Dihedral : 6.113 14.416 400 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.26 % Allowed : 21.29 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.39), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 2880) covalent geometry : angle 0.59435 ( 3900) hydrogen bonds : bond 0.03275 ( 13) hydrogen bonds : angle 5.22392 ( 39) =============================================================================== Job complete usr+sys time: 568.20 seconds wall clock time: 10 minutes 30.46 seconds (630.46 seconds total)