Starting phenix.real_space_refine on Wed Sep 17 12:21:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rx5_24725/09_2025/7rx5_24725.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx5_24725/09_2025/7rx5_24725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rx5_24725/09_2025/7rx5_24725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx5_24725/09_2025/7rx5_24725.map" model { file = "/net/cci-nas-00/data/ceres_data/7rx5_24725/09_2025/7rx5_24725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx5_24725/09_2025/7rx5_24725.cif" } resolution = 3.4 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= 0.003 sd= 0.068 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 5640 2.51 5 N 1720 2.21 5 O 1760 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: 9120 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Restraints were copied for chains: C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, A, V, W, X, Y, Z, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, a, b, c, d Time building chain proxies: 0.79, per 1000 atoms: 0.09 Number of scatterers: 9120 At special positions: 0 Unit cell: (89.64, 89.64, 105.84, 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 1760 8.00 N 1720 7.00 C 5640 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: 0.70 Conformation dependent library (CDL) restraints added in 438.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 100.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA D 7 " --> pdb=" O GLU D 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA E 7 " --> pdb=" O GLU E 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA F 7 " --> pdb=" O GLU F 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA G 7 " --> pdb=" O GLU G 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA I 7 " --> pdb=" O GLU I 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA J 7 " --> pdb=" O GLU J 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA L 7 " --> pdb=" O GLU L 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA M 7 " --> pdb=" O GLU M 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA N 7 " --> pdb=" O GLU N 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA O 7 " --> pdb=" O GLU O 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA P 7 " --> pdb=" O GLU P 3 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA Q 7 " --> pdb=" O GLU Q 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA R 7 " --> pdb=" O GLU R 3 " (cutoff:3.500A) Processing helix chain 'S' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA S 7 " --> pdb=" O GLU S 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA T 7 " --> pdb=" O GLU T 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA U 7 " --> pdb=" O GLU U 3 " (cutoff:3.500A) Processing helix chain 'V' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA V 7 " --> pdb=" O GLU V 3 " (cutoff:3.500A) Processing helix chain 'W' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA W 7 " --> pdb=" O GLU W 3 " (cutoff:3.500A) Processing helix chain 'X' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA X 7 " --> pdb=" O GLU X 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA Y 7 " --> pdb=" O GLU Y 3 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA Z 7 " --> pdb=" O GLU Z 3 " (cutoff:3.500A) Processing helix chain '0' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 0 7 " --> pdb=" O GLU 0 3 " (cutoff:3.500A) Processing helix chain '1' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 1 7 " --> pdb=" O GLU 1 3 " (cutoff:3.500A) Processing helix chain '2' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 2 7 " --> pdb=" O GLU 2 3 " (cutoff:3.500A) Processing helix chain '3' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 3 7 " --> pdb=" O GLU 3 3 " (cutoff:3.500A) Processing helix chain '4' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA 4 7 " --> pdb=" O GLU 4 3 " (cutoff:3.500A) Processing helix chain '5' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA 5 7 " --> pdb=" O GLU 5 3 " (cutoff:3.500A) Processing helix chain '6' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 6 7 " --> pdb=" O GLU 6 3 " (cutoff:3.500A) Processing helix chain '7' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 7 7 " --> pdb=" O GLU 7 3 " (cutoff:3.500A) Processing helix chain '8' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 8 7 " --> pdb=" O GLU 8 3 " (cutoff:3.500A) Processing helix chain '9' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 9 7 " --> pdb=" O GLU 9 3 " (cutoff:3.500A) Processing helix chain 'a' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA a 7 " --> pdb=" O GLU a 3 " (cutoff:3.500A) Processing helix chain 'b' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA b 7 " --> pdb=" O GLU b 3 " (cutoff:3.500A) Processing helix chain 'c' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA c 7 " --> pdb=" O GLU c 3 " (cutoff:3.500A) Processing helix chain 'd' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA d 7 " --> pdb=" O GLU d 3 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2880 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: 1.66 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1720 1.29 - 1.35: 1626 1.35 - 1.42: 374 1.42 - 1.48: 1240 1.48 - 1.54: 4200 Bond restraints: 9160 Sorted by residual: bond pdb=" N ILE B 18 " pdb=" CA ILE B 18 " ideal model delta sigma weight residual 1.461 1.466 -0.005 1.19e-02 7.06e+03 1.74e-01 bond pdb=" N ILE C 18 " pdb=" CA ILE C 18 " ideal model delta sigma weight residual 1.461 1.466 -0.005 1.19e-02 7.06e+03 1.74e-01 bond pdb=" N HIS F 22 " pdb=" CA HIS F 22 " ideal model delta sigma weight residual 1.459 1.464 -0.005 1.21e-02 6.83e+03 1.50e-01 bond pdb=" N HIS G 22 " pdb=" CA HIS G 22 " ideal model delta sigma weight residual 1.459 1.464 -0.005 1.21e-02 6.83e+03 1.50e-01 bond pdb=" N ILE N 18 " pdb=" CA ILE N 18 " ideal model delta sigma weight residual 1.461 1.465 -0.004 1.19e-02 7.06e+03 1.33e-01 ... (remaining 9155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.26: 9868 0.26 - 0.53: 1810 0.53 - 0.79: 438 0.79 - 1.05: 124 1.05 - 1.32: 40 Bond angle restraints: 12280 Sorted by residual: angle pdb=" C ILE N 25 " pdb=" CA ILE N 25 " pdb=" CB ILE N 25 " ideal model delta sigma weight residual 111.97 110.97 1.00 1.28e+00 6.10e-01 6.07e-01 angle pdb=" C ILE O 25 " pdb=" CA ILE O 25 " pdb=" CB ILE O 25 " ideal model delta sigma weight residual 111.97 110.97 1.00 1.28e+00 6.10e-01 6.07e-01 angle pdb=" C ILE 8 25 " pdb=" CA ILE 8 25 " pdb=" CB ILE 8 25 " ideal model delta sigma weight residual 111.97 110.98 0.99 1.28e+00 6.10e-01 5.95e-01 angle pdb=" C ILE 9 25 " pdb=" CA ILE 9 25 " pdb=" CB ILE 9 25 " ideal model delta sigma weight residual 111.97 110.98 0.99 1.28e+00 6.10e-01 5.95e-01 angle pdb=" C ILE c 25 " pdb=" CA ILE c 25 " pdb=" CB ILE c 25 " ideal model delta sigma weight residual 111.97 110.99 0.98 1.28e+00 6.10e-01 5.82e-01 ... (remaining 12275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.23: 4440 7.23 - 14.46: 680 14.46 - 21.68: 320 21.68 - 28.91: 200 28.91 - 36.14: 160 Dihedral angle restraints: 5800 sinusoidal: 2320 harmonic: 3480 Sorted by residual: dihedral pdb=" CB ARG 7 13 " pdb=" CG ARG 7 13 " pdb=" CD ARG 7 13 " pdb=" NE ARG 7 13 " ideal model delta sinusoidal sigma weight residual -180.00 -143.86 -36.14 3 1.50e+01 4.44e-03 6.24e+00 dihedral pdb=" CB ARG 6 13 " pdb=" CG ARG 6 13 " pdb=" CD ARG 6 13 " pdb=" NE ARG 6 13 " ideal model delta sinusoidal sigma weight residual -180.00 -143.86 -36.14 3 1.50e+01 4.44e-03 6.24e+00 dihedral pdb=" CB ARG B 13 " pdb=" CG ARG B 13 " pdb=" CD ARG B 13 " pdb=" NE ARG B 13 " ideal model delta sinusoidal sigma weight residual -180.00 -143.88 -36.12 3 1.50e+01 4.44e-03 6.23e+00 ... (remaining 5797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.017: 782 0.017 - 0.035: 440 0.035 - 0.052: 58 0.052 - 0.070: 40 0.070 - 0.087: 80 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CA ILE H 25 " pdb=" N ILE H 25 " pdb=" C ILE H 25 " pdb=" CB ILE H 25 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 1.89e-01 chirality pdb=" CA ILE I 25 " pdb=" N ILE I 25 " pdb=" C ILE I 25 " pdb=" CB ILE I 25 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 1.89e-01 chirality pdb=" CA ILE O 25 " pdb=" N ILE O 25 " pdb=" C ILE O 25 " pdb=" CB ILE O 25 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 1.86e-01 ... (remaining 1397 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 22 " 0.003 2.00e-02 2.50e+03 2.68e-03 1.07e-01 pdb=" CG HIS D 22 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS D 22 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS D 22 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS D 22 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS D 22 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 22 " 0.003 2.00e-02 2.50e+03 2.68e-03 1.07e-01 pdb=" CG HIS E 22 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS E 22 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 22 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS E 22 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS E 22 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS Y 22 " 0.002 2.00e-02 2.50e+03 2.65e-03 1.05e-01 pdb=" CG HIS Y 22 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS Y 22 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS Y 22 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS Y 22 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS Y 22 " 0.000 2.00e-02 2.50e+03 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2424 2.81 - 3.33: 9756 3.33 - 3.86: 15358 3.86 - 4.38: 18174 4.38 - 4.90: 29490 Nonbonded interactions: 75202 Sorted by model distance: nonbonded pdb=" OE1 GLN Y 29 " pdb=" NH1 ARG 0 13 " model vdw 2.288 3.120 nonbonded pdb=" OE1 GLN Z 29 " pdb=" NH1 ARG 1 13 " model vdw 2.288 3.120 nonbonded pdb=" OE1 GLN S 29 " pdb=" NH1 ARG U 13 " model vdw 2.288 3.120 nonbonded pdb=" OE1 GLN R 29 " pdb=" NH1 ARG T 13 " model vdw 2.288 3.120 nonbonded pdb=" OE1 GLN U 29 " pdb=" NH1 ARG V 13 " model vdw 2.288 3.120 ... (remaining 75197 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: 0.04 Found NCS groups: ncs_group { reference = 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' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'A' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.600 Find NCS groups from input model: 0.090 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.002 0.008 9160 Z= 0.096 Angle : 0.246 1.318 12280 Z= 0.156 Chirality : 0.029 0.087 1400 Planarity : 0.001 0.006 1640 Dihedral : 11.982 36.141 3480 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.54 (0.24), residues: 1080 helix: 2.95 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 17 TYR 0.002 0.001 TYR T 15 HIS 0.003 0.002 HIS Y 22 Details of bonding type rmsd covalent geometry : bond 0.00180 ( 9160) covalent geometry : angle 0.24609 (12280) hydrogen bonds : bond 0.11891 ( 960) hydrogen bonds : angle 3.11419 ( 2880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.342 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2085 time to fit residues: 20.1935 Evaluate side-chains 80 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.130143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.103922 restraints weight = 9174.323| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.00 r_work: 0.2904 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9160 Z= 0.118 Angle : 0.314 3.358 12280 Z= 0.179 Chirality : 0.030 0.099 1400 Planarity : 0.002 0.010 1640 Dihedral : 3.230 6.081 1240 Min Nonbonded Distance : 2.689 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.49 (0.23), residues: 1080 helix: 2.92 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 13 TYR 0.002 0.001 TYR J 15 HIS 0.003 0.002 HIS S 22 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9160) covalent geometry : angle 0.31432 (12280) hydrogen bonds : bond 0.03763 ( 960) hydrogen bonds : angle 2.99987 ( 2880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.578 Fit side-chains REVERT: D 24 GLU cc_start: 0.8255 (tp30) cc_final: 0.7987 (tp30) REVERT: E 24 GLU cc_start: 0.8300 (tp30) cc_final: 0.8033 (tp30) REVERT: 6 24 GLU cc_start: 0.8330 (tp30) cc_final: 0.7775 (tp30) REVERT: 7 24 GLU cc_start: 0.8347 (tp30) cc_final: 0.7791 (tp30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1998 time to fit residues: 19.5741 Evaluate side-chains 80 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.165581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.137689 restraints weight = 8841.471| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.11 r_work: 0.2824 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 9160 Z= 0.212 Angle : 0.357 2.589 12280 Z= 0.205 Chirality : 0.033 0.100 1400 Planarity : 0.002 0.020 1640 Dihedral : 3.216 6.368 1240 Min Nonbonded Distance : 2.689 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: 3.87 (0.23), residues: 1080 helix: 2.53 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 13 TYR 0.005 0.001 TYR J 15 HIS 0.004 0.002 HIS K 22 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 9160) covalent geometry : angle 0.35681 (12280) hydrogen bonds : bond 0.05190 ( 960) hydrogen bonds : angle 3.38004 ( 2880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.351 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2177 time to fit residues: 16.2064 Evaluate side-chains 62 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.169539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140486 restraints weight = 8904.082| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.18 r_work: 0.2855 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 9160 Z= 0.116 Angle : 0.269 1.817 12280 Z= 0.159 Chirality : 0.029 0.097 1400 Planarity : 0.001 0.010 1640 Dihedral : 3.173 6.193 1240 Min Nonbonded Distance : 2.691 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 4.49 (0.22), residues: 1080 helix: 2.92 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 13 TYR 0.002 0.001 TYR 8 15 HIS 0.003 0.002 HIS R 22 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9160) covalent geometry : angle 0.26948 (12280) hydrogen bonds : bond 0.03778 ( 960) hydrogen bonds : angle 3.05448 ( 2880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.348 Fit side-chains REVERT: D 24 GLU cc_start: 0.8497 (tp30) cc_final: 0.8099 (tp30) REVERT: E 24 GLU cc_start: 0.8502 (tp30) cc_final: 0.8108 (tp30) REVERT: 6 24 GLU cc_start: 0.8421 (tp30) cc_final: 0.8088 (tp30) REVERT: 7 24 GLU cc_start: 0.8440 (tp30) cc_final: 0.8105 (tp30) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2038 time to fit residues: 19.3198 Evaluate side-chains 78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.176415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.148760 restraints weight = 8805.962| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.12 r_work: 0.2904 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 9160 Z= 0.101 Angle : 0.261 2.728 12280 Z= 0.155 Chirality : 0.029 0.098 1400 Planarity : 0.001 0.006 1640 Dihedral : 3.111 6.029 1240 Min Nonbonded Distance : 2.692 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 5.07 (0.21), residues: 1080 helix: 3.27 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG W 13 TYR 0.002 0.000 TYR 9 15 HIS 0.003 0.001 HIS R 22 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 9160) covalent geometry : angle 0.26114 (12280) hydrogen bonds : bond 0.03414 ( 960) hydrogen bonds : angle 2.92202 ( 2880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.351 Fit side-chains REVERT: D 24 GLU cc_start: 0.8530 (tp30) cc_final: 0.8102 (tp30) REVERT: E 24 GLU cc_start: 0.8566 (tp30) cc_final: 0.8135 (tp30) REVERT: L 24 GLU cc_start: 0.8762 (tp30) cc_final: 0.8496 (tp30) REVERT: M 24 GLU cc_start: 0.8721 (tp30) cc_final: 0.8457 (tp30) REVERT: 7 24 GLU cc_start: 0.8416 (tp30) cc_final: 0.8204 (tp30) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2001 time to fit residues: 18.9444 Evaluate side-chains 78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.171710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144753 restraints weight = 8824.153| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.08 r_work: 0.2912 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9160 Z= 0.104 Angle : 0.265 3.973 12280 Z= 0.156 Chirality : 0.029 0.100 1400 Planarity : 0.001 0.007 1640 Dihedral : 3.085 6.002 1240 Min Nonbonded Distance : 2.693 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: 5.32 (0.21), residues: 1080 helix: 3.43 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG W 13 TYR 0.002 0.000 TYR 8 15 HIS 0.003 0.001 HIS R 22 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 9160) covalent geometry : angle 0.26518 (12280) hydrogen bonds : bond 0.03472 ( 960) hydrogen bonds : angle 2.91531 ( 2880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.413 Fit side-chains REVERT: D 24 GLU cc_start: 0.8543 (tp30) cc_final: 0.8105 (tp30) REVERT: E 24 GLU cc_start: 0.8568 (tp30) cc_final: 0.8130 (tp30) REVERT: L 24 GLU cc_start: 0.8747 (tp30) cc_final: 0.8485 (tp30) REVERT: M 24 GLU cc_start: 0.8708 (tp30) cc_final: 0.8449 (tp30) REVERT: 7 24 GLU cc_start: 0.8378 (tp30) cc_final: 0.8145 (tp30) REVERT: 8 24 GLU cc_start: 0.8472 (tp30) cc_final: 0.8258 (tp30) REVERT: 9 24 GLU cc_start: 0.8465 (tp30) cc_final: 0.8249 (tp30) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1956 time to fit residues: 18.5446 Evaluate side-chains 78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.174963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147281 restraints weight = 8764.343| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.10 r_work: 0.2884 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9160 Z= 0.126 Angle : 0.279 4.213 12280 Z= 0.162 Chirality : 0.030 0.097 1400 Planarity : 0.002 0.009 1640 Dihedral : 3.085 6.047 1240 Min Nonbonded Distance : 2.692 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: 5.26 (0.21), residues: 1080 helix: 3.39 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 13 TYR 0.002 0.000 TYR 8 15 HIS 0.003 0.002 HIS S 22 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9160) covalent geometry : angle 0.27854 (12280) hydrogen bonds : bond 0.03924 ( 960) hydrogen bonds : angle 3.02427 ( 2880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.342 Fit side-chains REVERT: 7 24 GLU cc_start: 0.8592 (tp30) cc_final: 0.8235 (tp30) REVERT: 8 24 GLU cc_start: 0.8581 (tp30) cc_final: 0.8335 (tp30) REVERT: 9 24 GLU cc_start: 0.8559 (tp30) cc_final: 0.8312 (tp30) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2017 time to fit residues: 17.9792 Evaluate side-chains 74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.0570 overall best weight: 1.1704 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.178162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150079 restraints weight = 8685.947| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.11 r_work: 0.2872 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9160 Z= 0.136 Angle : 0.288 4.437 12280 Z= 0.166 Chirality : 0.030 0.098 1400 Planarity : 0.002 0.011 1640 Dihedral : 3.101 6.095 1240 Min Nonbonded Distance : 2.693 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: 5.13 (0.21), residues: 1080 helix: 3.31 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG 4 17 TYR 0.002 0.001 TYR 8 15 HIS 0.003 0.002 HIS I 22 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9160) covalent geometry : angle 0.28832 (12280) hydrogen bonds : bond 0.04065 ( 960) hydrogen bonds : angle 3.07313 ( 2880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.293 Fit side-chains REVERT: 7 24 GLU cc_start: 0.8644 (tp30) cc_final: 0.8262 (tp30) REVERT: 8 24 GLU cc_start: 0.8559 (tp30) cc_final: 0.8322 (tp30) REVERT: 9 24 GLU cc_start: 0.8558 (tp30) cc_final: 0.8320 (tp30) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2075 time to fit residues: 18.0058 Evaluate side-chains 72 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 50 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 8 optimal weight: 9.9990 chunk 73 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.174571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146992 restraints weight = 8791.759| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.10 r_work: 0.2908 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9160 Z= 0.097 Angle : 0.257 3.152 12280 Z= 0.152 Chirality : 0.029 0.097 1400 Planarity : 0.001 0.008 1640 Dihedral : 3.099 6.004 1240 Min Nonbonded Distance : 2.694 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: 5.48 (0.21), residues: 1080 helix: 3.53 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 13 TYR 0.002 0.000 TYR 8 15 HIS 0.002 0.001 HIS R 22 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 9160) covalent geometry : angle 0.25702 (12280) hydrogen bonds : bond 0.03322 ( 960) hydrogen bonds : angle 2.88987 ( 2880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.226 Fit side-chains REVERT: D 24 GLU cc_start: 0.8500 (tp30) cc_final: 0.8191 (tp30) REVERT: E 24 GLU cc_start: 0.8521 (tp30) cc_final: 0.8210 (tp30) REVERT: L 24 GLU cc_start: 0.8752 (tp30) cc_final: 0.8491 (tp30) REVERT: M 24 GLU cc_start: 0.8683 (tp30) cc_final: 0.8427 (tp30) REVERT: R 22 HIS cc_start: 0.8744 (m-70) cc_final: 0.8511 (m170) REVERT: S 22 HIS cc_start: 0.8753 (m-70) cc_final: 0.8519 (m170) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1945 time to fit residues: 18.8877 Evaluate side-chains 80 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.162266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133336 restraints weight = 8853.334| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.20 r_work: 0.2791 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 9160 Z= 0.208 Angle : 0.364 4.915 12280 Z= 0.204 Chirality : 0.033 0.098 1400 Planarity : 0.002 0.020 1640 Dihedral : 3.128 6.427 1240 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 4.65 (0.22), residues: 1080 helix: 3.02 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 4 17 TYR 0.003 0.001 TYR 9 15 HIS 0.004 0.002 HIS R 22 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 9160) covalent geometry : angle 0.36372 (12280) hydrogen bonds : bond 0.04969 ( 960) hydrogen bonds : angle 3.29507 ( 2880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2114 time to fit residues: 16.3106 Evaluate side-chains 64 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.0170 chunk 32 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.176510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149221 restraints weight = 8683.027| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.10 r_work: 0.2912 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9160 Z= 0.103 Angle : 0.293 4.647 12280 Z= 0.169 Chirality : 0.029 0.097 1400 Planarity : 0.001 0.010 1640 Dihedral : 3.142 6.146 1240 Min Nonbonded Distance : 2.693 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 5.30 (0.21), residues: 1080 helix: 3.42 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 13 TYR 0.002 0.001 TYR 8 15 HIS 0.002 0.001 HIS Y 22 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 9160) covalent geometry : angle 0.29290 (12280) hydrogen bonds : bond 0.03340 ( 960) hydrogen bonds : angle 2.92837 ( 2880) =============================================================================== Job complete usr+sys time: 1859.78 seconds wall clock time: 32 minutes 38.30 seconds (1958.30 seconds total)