Starting phenix.real_space_refine on Fri May 9 15:51:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1k_41815/05_2025/8u1k_41815.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1k_41815/05_2025/8u1k_41815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u1k_41815/05_2025/8u1k_41815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1k_41815/05_2025/8u1k_41815.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1k_41815/05_2025/8u1k_41815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1k_41815/05_2025/8u1k_41815.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 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 1970 2.51 5 N 500 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3060 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.73, per 1000 atoms: 0.57 Number of scatterers: 3060 At special positions: 0 Unit cell: (58.38, 57.546, 118.428, 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 500 7.00 C 1970 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: 0.77 Conformation dependent library (CDL) restraints added in 383.3 milliseconds 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 820 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 3 through 5 No H-bonds generated for 'chain 'A' and resid 3 through 5' Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 30 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 5 No H-bonds generated for 'chain 'B' and resid 3 through 5' Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 5 No H-bonds generated for 'chain 'D' and resid 3 through 5' Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR D 30 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 5 No H-bonds generated for 'chain 'E' and resid 3 through 5' Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR E 30 " --> pdb=" O THR E 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 5 No H-bonds generated for 'chain 'F' and resid 3 through 5' Processing helix chain 'F' and resid 6 through 11 Processing helix chain 'F' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR F 30 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR F 41 " --> pdb=" O ALA F 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 5 No H-bonds generated for 'chain 'G' and resid 3 through 5' Processing helix chain 'G' and resid 6 through 11 Processing helix chain 'G' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR G 30 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 5 No H-bonds generated for 'chain 'H' and resid 3 through 5' Processing helix chain 'H' and resid 6 through 11 Processing helix chain 'H' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR H 30 " --> pdb=" O THR H 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 5 No H-bonds generated for 'chain 'I' and resid 3 through 5' Processing helix chain 'I' and resid 6 through 11 Processing helix chain 'I' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR I 30 " --> pdb=" O THR I 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR I 41 " --> pdb=" O ALA I 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 5 No H-bonds generated for 'chain 'J' and resid 3 through 5' Processing helix chain 'J' and resid 6 through 11 Processing helix chain 'J' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR J 30 " --> pdb=" O THR J 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR J 41 " --> pdb=" O ALA J 37 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 630 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: 0.74 Time building geometry restraints manager: 0.90 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: 480 1.29 - 1.35: 480 1.35 - 1.42: 140 1.42 - 1.48: 550 1.48 - 1.54: 1420 Bond restraints: 3070 Sorted by residual: bond pdb=" CA ALA E 38 " pdb=" C ALA E 38 " ideal model delta sigma weight residual 1.524 1.516 0.009 1.29e-02 6.01e+03 4.38e-01 bond pdb=" CA ALA A 38 " pdb=" C ALA A 38 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.29e-02 6.01e+03 4.00e-01 bond pdb=" CA ALA C 38 " pdb=" C ALA C 38 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.29e-02 6.01e+03 3.96e-01 bond pdb=" CA ALA I 38 " pdb=" C ALA I 38 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.29e-02 6.01e+03 3.85e-01 bond pdb=" N ALA F 38 " pdb=" CA ALA F 38 " ideal model delta sigma weight residual 1.459 1.451 0.008 1.24e-02 6.50e+03 3.84e-01 ... (remaining 3065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.65: 3507 0.65 - 1.30: 468 1.30 - 1.95: 195 1.95 - 2.60: 30 2.60 - 3.25: 20 Bond angle restraints: 4220 Sorted by residual: angle pdb=" N ILE G 4 " pdb=" CA ILE G 4 " pdb=" C ILE G 4 " ideal model delta sigma weight residual 109.34 112.59 -3.25 2.08e+00 2.31e-01 2.44e+00 angle pdb=" N ILE F 4 " pdb=" CA ILE F 4 " pdb=" C ILE F 4 " ideal model delta sigma weight residual 109.34 112.59 -3.25 2.08e+00 2.31e-01 2.43e+00 angle pdb=" N ILE A 4 " pdb=" CA ILE A 4 " pdb=" C ILE A 4 " ideal model delta sigma weight residual 109.34 112.58 -3.24 2.08e+00 2.31e-01 2.43e+00 angle pdb=" N ILE H 4 " pdb=" CA ILE H 4 " pdb=" C ILE H 4 " ideal model delta sigma weight residual 109.34 112.58 -3.24 2.08e+00 2.31e-01 2.42e+00 angle pdb=" N ILE B 4 " pdb=" CA ILE B 4 " pdb=" C ILE B 4 " ideal model delta sigma weight residual 109.34 112.56 -3.22 2.08e+00 2.31e-01 2.40e+00 ... (remaining 4215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.83: 1500 9.83 - 19.66: 140 19.66 - 29.49: 70 29.49 - 39.32: 30 39.32 - 49.16: 30 Dihedral angle restraints: 1770 sinusoidal: 500 harmonic: 1270 Sorted by residual: dihedral pdb=" N ILE A 4 " pdb=" CA ILE A 4 " pdb=" CB ILE A 4 " pdb=" CG1 ILE A 4 " ideal model delta sinusoidal sigma weight residual -60.00 -10.84 -49.16 3 1.50e+01 4.44e-03 8.74e+00 dihedral pdb=" N ILE B 4 " pdb=" CA ILE B 4 " pdb=" CB ILE B 4 " pdb=" CG1 ILE B 4 " ideal model delta sinusoidal sigma weight residual -60.00 -10.85 -49.15 3 1.50e+01 4.44e-03 8.74e+00 dihedral pdb=" N ILE I 4 " pdb=" CA ILE I 4 " pdb=" CB ILE I 4 " pdb=" CG1 ILE I 4 " ideal model delta sinusoidal sigma weight residual -60.00 -10.90 -49.10 3 1.50e+01 4.44e-03 8.73e+00 ... (remaining 1767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 282 0.021 - 0.041: 173 0.041 - 0.062: 95 0.062 - 0.083: 50 0.083 - 0.103: 40 Chirality restraints: 640 Sorted by residual: chirality pdb=" CA THR F 30 " pdb=" N THR F 30 " pdb=" C THR F 30 " pdb=" CB THR F 30 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.10 2.00e-01 2.50e+01 2.67e-01 chirality pdb=" CA THR A 30 " pdb=" N THR A 30 " pdb=" C THR A 30 " pdb=" CB THR A 30 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.10 2.00e-01 2.50e+01 2.59e-01 chirality pdb=" CA THR J 30 " pdb=" N THR J 30 " pdb=" C THR J 30 " pdb=" CB THR J 30 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.10 2.00e-01 2.50e+01 2.57e-01 ... (remaining 637 not shown) Planarity restraints: 490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 25 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C GLY F 25 " -0.026 2.00e-02 2.50e+03 pdb=" O GLY F 25 " 0.010 2.00e-02 2.50e+03 pdb=" N THR F 26 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY J 25 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C GLY J 25 " -0.026 2.00e-02 2.50e+03 pdb=" O GLY J 25 " 0.010 2.00e-02 2.50e+03 pdb=" N THR J 26 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 25 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C GLY G 25 " 0.026 2.00e-02 2.50e+03 pdb=" O GLY G 25 " -0.010 2.00e-02 2.50e+03 pdb=" N THR G 26 " -0.009 2.00e-02 2.50e+03 ... (remaining 487 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 509 2.74 - 3.28: 3380 3.28 - 3.82: 5155 3.82 - 4.36: 5996 4.36 - 4.90: 9519 Nonbonded interactions: 24559 Sorted by model distance: nonbonded pdb=" O ARG D 29 " pdb=" OG1 THR D 33 " model vdw 2.206 3.040 nonbonded pdb=" O ARG A 29 " pdb=" OG1 THR A 33 " model vdw 2.206 3.040 nonbonded pdb=" O ARG J 29 " pdb=" OG1 THR J 33 " model vdw 2.206 3.040 nonbonded pdb=" O ARG H 29 " pdb=" OG1 THR H 33 " model vdw 2.207 3.040 nonbonded pdb=" O ARG B 29 " pdb=" OG1 THR B 33 " model vdw 2.207 3.040 ... (remaining 24554 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 1.360 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.070 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 15.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 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 0.018 3070 Z= 0.203 Angle : 0.609 3.251 4220 Z= 0.377 Chirality : 0.040 0.103 640 Planarity : 0.003 0.015 490 Dihedral : 13.638 49.155 950 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.33 % Allowed : 10.00 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.99 (0.23), residues: 430 helix: -3.55 (0.17), residues: 340 sheet: None (None), residues: 0 loop : -4.60 (0.29), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.001 PHE B 32 TYR 0.003 0.001 TYR C 6 ARG 0.002 0.001 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.05959 ( 210) hydrogen bonds : angle 4.99398 ( 630) covalent geometry : bond 0.00371 ( 3070) covalent geometry : angle 0.60898 ( 4220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 215 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8181 (m) cc_final: 0.7831 (p) REVERT: A 23 THR cc_start: 0.7918 (m) cc_final: 0.7493 (p) REVERT: A 24 LEU cc_start: 0.8794 (tp) cc_final: 0.8574 (tp) REVERT: A 26 THR cc_start: 0.7855 (t) cc_final: 0.7535 (m) REVERT: A 29 ARG cc_start: 0.6708 (mtt180) cc_final: 0.6429 (mtt-85) REVERT: B 18 VAL cc_start: 0.8584 (t) cc_final: 0.8291 (m) REVERT: B 23 THR cc_start: 0.7839 (m) cc_final: 0.7286 (p) REVERT: B 24 LEU cc_start: 0.8771 (tp) cc_final: 0.8388 (tp) REVERT: B 34 LYS cc_start: 0.7539 (mtmm) cc_final: 0.7291 (mtmm) REVERT: C 18 VAL cc_start: 0.8548 (t) cc_final: 0.8287 (m) REVERT: C 23 THR cc_start: 0.7859 (m) cc_final: 0.7351 (p) REVERT: D 4 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8137 (mp) REVERT: D 18 VAL cc_start: 0.8513 (t) cc_final: 0.8287 (m) REVERT: D 23 THR cc_start: 0.7891 (m) cc_final: 0.7252 (p) REVERT: D 24 LEU cc_start: 0.8740 (tp) cc_final: 0.8516 (tp) REVERT: D 27 ASN cc_start: 0.7039 (m-40) cc_final: 0.6792 (m110) REVERT: E 18 VAL cc_start: 0.8614 (t) cc_final: 0.8289 (m) REVERT: E 27 ASN cc_start: 0.7090 (m-40) cc_final: 0.6838 (m110) REVERT: F 23 THR cc_start: 0.7904 (m) cc_final: 0.7425 (p) REVERT: F 26 THR cc_start: 0.8031 (t) cc_final: 0.7751 (m) REVERT: F 29 ARG cc_start: 0.6889 (mtt180) cc_final: 0.6464 (mtt-85) REVERT: G 23 THR cc_start: 0.7990 (m) cc_final: 0.7534 (p) REVERT: G 24 LEU cc_start: 0.8864 (tp) cc_final: 0.8451 (tt) REVERT: G 26 THR cc_start: 0.8044 (t) cc_final: 0.7399 (m) REVERT: G 29 ARG cc_start: 0.6552 (mtt180) cc_final: 0.6245 (mtt-85) REVERT: H 23 THR cc_start: 0.8003 (m) cc_final: 0.7600 (p) REVERT: H 24 LEU cc_start: 0.8858 (tp) cc_final: 0.8618 (tp) REVERT: I 23 THR cc_start: 0.7899 (m) cc_final: 0.7374 (p) REVERT: I 24 LEU cc_start: 0.8800 (tp) cc_final: 0.8525 (tp) REVERT: J 18 VAL cc_start: 0.8554 (t) cc_final: 0.8304 (m) REVERT: J 23 THR cc_start: 0.7933 (m) cc_final: 0.7479 (p) REVERT: J 24 LEU cc_start: 0.8856 (tp) cc_final: 0.8403 (tt) REVERT: J 34 LYS cc_start: 0.7465 (mtmm) cc_final: 0.7102 (mtmm) outliers start: 10 outliers final: 6 residues processed: 224 average time/residue: 0.1292 time to fit residues: 34.4709 Evaluate side-chains 222 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain J residue 4 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.099556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.089867 restraints weight = 5751.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.092059 restraints weight = 2704.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.093513 restraints weight = 1582.059| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3070 Z= 0.127 Angle : 0.507 4.625 4220 Z= 0.286 Chirality : 0.038 0.099 640 Planarity : 0.003 0.033 490 Dihedral : 8.630 55.240 474 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 10.00 % Allowed : 32.00 % Favored : 58.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.32), residues: 430 helix: -2.43 (0.24), residues: 340 sheet: None (None), residues: 0 loop : -3.74 (0.41), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE I 32 TYR 0.007 0.002 TYR H 6 ARG 0.008 0.001 ARG E 29 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 210) hydrogen bonds : angle 4.45657 ( 630) covalent geometry : bond 0.00241 ( 3070) covalent geometry : angle 0.50661 ( 4220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8070 (m) cc_final: 0.7817 (p) REVERT: A 18 VAL cc_start: 0.8775 (t) cc_final: 0.8521 (m) REVERT: A 23 THR cc_start: 0.7846 (m) cc_final: 0.7381 (p) REVERT: B 23 THR cc_start: 0.7833 (m) cc_final: 0.7316 (p) REVERT: C 4 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7909 (mp) REVERT: C 23 THR cc_start: 0.7736 (m) cc_final: 0.7276 (p) REVERT: C 28 LEU cc_start: 0.8719 (tp) cc_final: 0.8455 (tt) REVERT: D 18 VAL cc_start: 0.8595 (t) cc_final: 0.8317 (m) REVERT: D 23 THR cc_start: 0.7862 (m) cc_final: 0.7242 (p) REVERT: D 27 ASN cc_start: 0.6816 (m-40) cc_final: 0.6532 (m110) REVERT: E 18 VAL cc_start: 0.8674 (t) cc_final: 0.8349 (m) REVERT: F 23 THR cc_start: 0.7849 (m) cc_final: 0.7366 (p) REVERT: F 26 THR cc_start: 0.8019 (t) cc_final: 0.7664 (m) REVERT: G 23 THR cc_start: 0.7960 (m) cc_final: 0.7486 (p) REVERT: G 24 LEU cc_start: 0.8690 (tp) cc_final: 0.8378 (tt) REVERT: G 26 THR cc_start: 0.8117 (t) cc_final: 0.7676 (t) REVERT: H 23 THR cc_start: 0.7907 (m) cc_final: 0.7495 (p) REVERT: H 24 LEU cc_start: 0.8826 (tp) cc_final: 0.8583 (tp) REVERT: I 23 THR cc_start: 0.7695 (m) cc_final: 0.7237 (p) REVERT: I 24 LEU cc_start: 0.8735 (tp) cc_final: 0.8501 (tp) REVERT: J 18 VAL cc_start: 0.8633 (t) cc_final: 0.8405 (m) REVERT: J 23 THR cc_start: 0.7721 (m) cc_final: 0.7344 (p) REVERT: J 24 LEU cc_start: 0.8769 (tp) cc_final: 0.8331 (tt) outliers start: 30 outliers final: 24 residues processed: 219 average time/residue: 0.1257 time to fit residues: 33.0028 Evaluate side-chains 237 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 17 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.100308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.090536 restraints weight = 5758.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.092713 restraints weight = 2736.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.094133 restraints weight = 1620.462| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3070 Z= 0.167 Angle : 0.557 6.577 4220 Z= 0.312 Chirality : 0.040 0.116 640 Planarity : 0.004 0.043 490 Dihedral : 6.773 47.526 470 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 13.33 % Allowed : 31.33 % Favored : 55.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.31), residues: 430 helix: -2.50 (0.23), residues: 340 sheet: None (None), residues: 0 loop : -3.72 (0.36), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE H 32 TYR 0.009 0.001 TYR D 6 ARG 0.009 0.001 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 210) hydrogen bonds : angle 4.49031 ( 630) covalent geometry : bond 0.00305 ( 3070) covalent geometry : angle 0.55682 ( 4220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8112 (m) cc_final: 0.7833 (p) REVERT: A 23 THR cc_start: 0.7895 (m) cc_final: 0.7418 (p) REVERT: B 18 VAL cc_start: 0.8702 (t) cc_final: 0.8473 (m) REVERT: B 23 THR cc_start: 0.7984 (m) cc_final: 0.7530 (p) REVERT: C 23 THR cc_start: 0.7808 (m) cc_final: 0.7330 (p) REVERT: D 18 VAL cc_start: 0.8617 (t) cc_final: 0.8272 (m) REVERT: D 23 THR cc_start: 0.7864 (m) cc_final: 0.7231 (p) REVERT: D 24 LEU cc_start: 0.8535 (tp) cc_final: 0.7666 (mm) REVERT: D 27 ASN cc_start: 0.6808 (m-40) cc_final: 0.6449 (m110) REVERT: E 18 VAL cc_start: 0.8545 (t) cc_final: 0.8258 (m) REVERT: F 23 THR cc_start: 0.7814 (m) cc_final: 0.7208 (p) REVERT: G 22 THR cc_start: 0.8622 (m) cc_final: 0.8282 (p) REVERT: G 23 THR cc_start: 0.7935 (m) cc_final: 0.7312 (p) REVERT: G 24 LEU cc_start: 0.8537 (tp) cc_final: 0.8267 (tt) REVERT: H 23 THR cc_start: 0.7949 (m) cc_final: 0.7555 (p) REVERT: H 24 LEU cc_start: 0.8824 (tp) cc_final: 0.8588 (tp) REVERT: I 23 THR cc_start: 0.7755 (m) cc_final: 0.7335 (p) REVERT: I 24 LEU cc_start: 0.8779 (tp) cc_final: 0.8361 (tt) REVERT: I 39 VAL cc_start: 0.8493 (p) cc_final: 0.8267 (t) REVERT: J 18 VAL cc_start: 0.8606 (t) cc_final: 0.8402 (m) REVERT: J 23 THR cc_start: 0.7739 (m) cc_final: 0.7456 (p) REVERT: J 24 LEU cc_start: 0.8789 (tp) cc_final: 0.8338 (tt) REVERT: J 34 LYS cc_start: 0.7411 (mtmt) cc_final: 0.7113 (mtmm) outliers start: 40 outliers final: 31 residues processed: 223 average time/residue: 0.1306 time to fit residues: 34.9741 Evaluate side-chains 246 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 27 ASN J 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.101007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.090724 restraints weight = 5854.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092979 restraints weight = 2760.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094402 restraints weight = 1619.452| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3070 Z= 0.171 Angle : 0.560 5.811 4220 Z= 0.315 Chirality : 0.041 0.140 640 Planarity : 0.005 0.060 490 Dihedral : 6.262 52.421 468 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 13.33 % Allowed : 34.67 % Favored : 52.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.31), residues: 430 helix: -2.44 (0.23), residues: 340 sheet: None (None), residues: 0 loop : -3.63 (0.34), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE B 32 TYR 0.007 0.001 TYR D 6 ARG 0.008 0.001 ARG F 29 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 210) hydrogen bonds : angle 4.43835 ( 630) covalent geometry : bond 0.00318 ( 3070) covalent geometry : angle 0.56008 ( 4220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8072 (m) cc_final: 0.7794 (p) REVERT: A 23 THR cc_start: 0.7888 (m) cc_final: 0.7436 (p) REVERT: B 18 VAL cc_start: 0.8730 (t) cc_final: 0.8510 (m) REVERT: B 23 THR cc_start: 0.8019 (m) cc_final: 0.7621 (p) REVERT: C 23 THR cc_start: 0.7810 (m) cc_final: 0.7327 (p) REVERT: D 18 VAL cc_start: 0.8591 (t) cc_final: 0.8234 (m) REVERT: D 23 THR cc_start: 0.7877 (m) cc_final: 0.7043 (p) REVERT: D 24 LEU cc_start: 0.8409 (tp) cc_final: 0.7482 (mm) REVERT: D 27 ASN cc_start: 0.6574 (m-40) cc_final: 0.6109 (m110) REVERT: E 18 VAL cc_start: 0.8470 (t) cc_final: 0.8166 (m) REVERT: E 27 ASN cc_start: 0.7147 (m-40) cc_final: 0.6790 (m110) REVERT: F 23 THR cc_start: 0.7985 (m) cc_final: 0.7502 (p) REVERT: F 24 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8349 (tt) REVERT: G 23 THR cc_start: 0.7972 (m) cc_final: 0.7464 (p) REVERT: G 24 LEU cc_start: 0.8595 (tp) cc_final: 0.8345 (tt) REVERT: H 23 THR cc_start: 0.7953 (m) cc_final: 0.7572 (p) REVERT: H 24 LEU cc_start: 0.8824 (tp) cc_final: 0.8589 (tp) REVERT: I 23 THR cc_start: 0.7708 (m) cc_final: 0.7262 (p) REVERT: I 24 LEU cc_start: 0.8755 (tp) cc_final: 0.8326 (tt) REVERT: I 39 VAL cc_start: 0.8511 (p) cc_final: 0.8291 (t) REVERT: J 2 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7406 (p) REVERT: J 23 THR cc_start: 0.7735 (m) cc_final: 0.7408 (p) REVERT: J 24 LEU cc_start: 0.8805 (tp) cc_final: 0.8366 (tt) REVERT: J 34 LYS cc_start: 0.7362 (mtmt) cc_final: 0.7057 (mtmm) outliers start: 40 outliers final: 34 residues processed: 222 average time/residue: 0.1273 time to fit residues: 33.8953 Evaluate side-chains 249 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 15 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.757 > 50: distance: 46 - 72: 14.694 distance: 57 - 79: 13.840 distance: 67 - 72: 12.560 distance: 72 - 73: 11.052 distance: 73 - 74: 5.584 distance: 73 - 76: 13.477 distance: 74 - 75: 16.922 distance: 74 - 79: 10.249 distance: 76 - 77: 14.479 distance: 76 - 78: 15.335 distance: 79 - 80: 3.687 distance: 80 - 81: 5.932 distance: 80 - 83: 11.220 distance: 81 - 82: 5.952 distance: 81 - 84: 3.974 distance: 84 - 85: 8.092 distance: 85 - 86: 8.058 distance: 85 - 88: 10.405 distance: 86 - 87: 11.251 distance: 86 - 92: 8.402 distance: 88 - 89: 19.475 distance: 89 - 90: 13.589 distance: 89 - 91: 13.119 distance: 92 - 93: 15.524 distance: 93 - 94: 19.952 distance: 93 - 96: 11.327 distance: 94 - 95: 13.676 distance: 94 - 100: 15.786 distance: 96 - 97: 21.301 distance: 96 - 98: 9.188 distance: 97 - 99: 21.046 distance: 100 - 101: 13.766 distance: 101 - 102: 14.973 distance: 101 - 104: 15.646 distance: 102 - 103: 11.283 distance: 102 - 105: 16.621 distance: 105 - 106: 5.685 distance: 106 - 107: 4.298 distance: 107 - 108: 7.986 distance: 107 - 112: 9.723 distance: 109 - 110: 20.607 distance: 109 - 111: 15.140 distance: 112 - 113: 6.880 distance: 113 - 116: 21.880 distance: 114 - 115: 9.668 distance: 116 - 117: 23.055 distance: 116 - 118: 13.167 distance: 119 - 120: 8.528 distance: 120 - 121: 10.490 distance: 120 - 123: 3.954 distance: 121 - 122: 19.390 distance: 121 - 127: 12.582 distance: 122 - 146: 21.856 distance: 123 - 124: 6.170 distance: 123 - 125: 4.805 distance: 124 - 126: 8.975 distance: 127 - 128: 18.262 distance: 128 - 129: 27.173 distance: 128 - 131: 13.290 distance: 129 - 130: 23.675 distance: 129 - 134: 23.916 distance: 130 - 153: 20.137 distance: 131 - 132: 29.356 distance: 131 - 133: 14.513 distance: 134 - 135: 31.272 distance: 135 - 136: 5.792 distance: 135 - 138: 23.692 distance: 136 - 137: 12.505 distance: 136 - 141: 9.689 distance: 138 - 139: 14.837 distance: 138 - 140: 16.435