Starting phenix.real_space_refine on Thu Jul 18 23:54:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx3_40825/07_2024/8sx3_40825.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx3_40825/07_2024/8sx3_40825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx3_40825/07_2024/8sx3_40825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx3_40825/07_2024/8sx3_40825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx3_40825/07_2024/8sx3_40825.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx3_40825/07_2024/8sx3_40825.cif" } resolution = 4.0 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= 0.000 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 3059 2.51 5 N 816 2.21 5 O 924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "L TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 90": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4816 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 913 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "B" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "C" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1236 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "H" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1016 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 121} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.87, per 1000 atoms: 0.80 Number of scatterers: 4816 At special positions: 0 Unit cell: (55.825, 67.425, 122.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 924 8.00 N 816 7.00 C 3059 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 86 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN C 74 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 850.6 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 18.9% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 63 through 67 removed outlier: 5.728A pdb=" N SER A 67 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.758A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 21 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 97 through 113 Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 125 through 140 removed outlier: 3.980A pdb=" N ALA C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 64 through 67 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'L' and resid 25 through 28 Processing helix chain 'L' and resid 77 through 81 removed outlier: 3.509A pdb=" N ASP L 81 " --> pdb=" O ALA L 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.709A pdb=" N VAL A 36 " --> pdb=" O HIS A 52 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N HIS A 52 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TRP A 38 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS A 52 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 60 " --> pdb=" O HIS A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.837A pdb=" N LEU B 11 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU B 105 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA B 13 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 42 removed outlier: 7.251A pdb=" N GLY C 48 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N PHE C 91 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA C 50 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU C 93 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N LYS C 71 " --> pdb=" O PRO C 86 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ARG C 88 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ARG C 154 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL C 66 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU C 156 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE C 68 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.597A pdb=" N TRP H 33 " --> pdb=" O THR H 101 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.044A pdb=" N CYS H 98 " --> pdb=" O TRP H 121 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TRP H 121 " --> pdb=" O CYS H 98 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG H 100 " --> pdb=" O GLN H 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'L' and resid 8 through 12 removed outlier: 6.296A pdb=" N GLN L 35 " --> pdb=" O LEU L 44 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU L 44 " --> pdb=" O GLN L 35 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 12 213 hydrogen bonds defined for protein. 525 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: 1.30 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 788 1.27 - 1.41: 1288 1.41 - 1.55: 2767 1.55 - 1.69: 64 1.69 - 1.82: 26 Bond restraints: 4933 Sorted by residual: bond pdb=" CG PRO C 141 " pdb=" CD PRO C 141 " ideal model delta sigma weight residual 1.503 1.131 0.372 3.40e-02 8.65e+02 1.20e+02 bond pdb=" N PRO C 141 " pdb=" CD PRO C 141 " ideal model delta sigma weight residual 1.473 1.554 -0.081 1.40e-02 5.10e+03 3.36e+01 bond pdb=" CB PRO C 82 " pdb=" CG PRO C 82 " ideal model delta sigma weight residual 1.492 1.658 -0.166 5.00e-02 4.00e+02 1.10e+01 bond pdb=" CB PRO C 141 " pdb=" CG PRO C 141 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.08e+00 bond pdb=" CB MET C 124 " pdb=" CG MET C 124 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.60e+00 ... (remaining 4928 not shown) Histogram of bond angle deviations from ideal: 86.58 - 96.14: 3 96.14 - 105.70: 117 105.70 - 115.25: 2846 115.25 - 124.81: 3549 124.81 - 134.37: 178 Bond angle restraints: 6693 Sorted by residual: angle pdb=" CA PRO C 141 " pdb=" N PRO C 141 " pdb=" CD PRO C 141 " ideal model delta sigma weight residual 112.00 94.70 17.30 1.40e+00 5.10e-01 1.53e+02 angle pdb=" N PRO C 141 " pdb=" CD PRO C 141 " pdb=" CG PRO C 141 " ideal model delta sigma weight residual 103.20 86.58 16.62 1.50e+00 4.44e-01 1.23e+02 angle pdb=" CA PRO C 82 " pdb=" N PRO C 82 " pdb=" CD PRO C 82 " ideal model delta sigma weight residual 112.00 99.04 12.96 1.40e+00 5.10e-01 8.57e+01 angle pdb=" CA PRO C 141 " pdb=" CB PRO C 141 " pdb=" CG PRO C 141 " ideal model delta sigma weight residual 104.50 90.52 13.98 1.90e+00 2.77e-01 5.41e+01 angle pdb=" CA TYR L 47 " pdb=" CB TYR L 47 " pdb=" CG TYR L 47 " ideal model delta sigma weight residual 113.90 122.48 -8.58 1.80e+00 3.09e-01 2.27e+01 ... (remaining 6688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 2625 17.91 - 35.81: 217 35.81 - 53.72: 61 53.72 - 71.62: 10 71.62 - 89.53: 3 Dihedral angle restraints: 2916 sinusoidal: 1176 harmonic: 1740 Sorted by residual: dihedral pdb=" CA PHE H 29 " pdb=" C PHE H 29 " pdb=" N ASP H 30 " pdb=" CA ASP H 30 " ideal model delta harmonic sigma weight residual 180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CB GLU L 6 " pdb=" CG GLU L 6 " pdb=" CD GLU L 6 " pdb=" OE1 GLU L 6 " ideal model delta sinusoidal sigma weight residual 0.00 89.53 -89.53 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASN H 79 " pdb=" CB ASN H 79 " pdb=" CG ASN H 79 " pdb=" OD1 ASN H 79 " ideal model delta sinusoidal sigma weight residual 120.00 -172.97 -67.03 2 2.00e+01 2.50e-03 1.02e+01 ... (remaining 2913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 532 0.069 - 0.138: 161 0.138 - 0.207: 28 0.207 - 0.275: 2 0.275 - 0.344: 2 Chirality restraints: 725 Sorted by residual: chirality pdb=" CA PRO C 82 " pdb=" N PRO C 82 " pdb=" C PRO C 82 " pdb=" CB PRO C 82 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA PRO C 141 " pdb=" N PRO C 141 " pdb=" C PRO C 141 " pdb=" CB PRO C 141 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE A 71 " pdb=" CA ILE A 71 " pdb=" CG1 ILE A 71 " pdb=" CG2 ILE A 71 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 722 not shown) Planarity restraints: 858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 35 " 0.042 2.00e-02 2.50e+03 3.03e-02 2.30e+01 pdb=" CG TRP B 35 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP B 35 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 35 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 35 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 35 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 35 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 35 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 35 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 111 " -0.081 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO H 112 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO H 112 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO H 112 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 140 " 0.087 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO C 141 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO C 141 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 141 " 0.063 5.00e-02 4.00e+02 ... (remaining 855 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 156 2.70 - 3.25: 4474 3.25 - 3.80: 7562 3.80 - 4.35: 9516 4.35 - 4.90: 15908 Nonbonded interactions: 37616 Sorted by model distance: nonbonded pdb=" O GLY L 75 " pdb=" NE2 GLN L 77 " model vdw 2.144 2.520 nonbonded pdb=" OD1 ASP A 91 " pdb=" OH TYR A 95 " model vdw 2.157 2.440 nonbonded pdb=" NE2 GLN A 13 " pdb=" O PRO A 14 " model vdw 2.201 2.520 nonbonded pdb=" NE2 GLN A 13 " pdb=" OE1 GLN A 16 " model vdw 2.245 2.520 nonbonded pdb=" OH TYR A 104 " pdb=" NH1 ARG C 131 " model vdw 2.264 2.520 ... (remaining 37611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.900 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 0.010 0.372 4933 Z= 0.616 Angle : 1.446 17.297 6693 Z= 0.795 Chirality : 0.066 0.344 725 Planarity : 0.011 0.120 857 Dihedral : 14.594 89.530 1802 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 23.26 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.92 (0.33), residues: 604 helix: 0.20 (0.53), residues: 75 sheet: 1.06 (0.34), residues: 212 loop : 0.54 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.005 TRP B 35 HIS 0.016 0.003 HIS L 29 PHE 0.063 0.007 PHE H 107 TYR 0.064 0.006 TYR L 85 ARG 0.018 0.002 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 TYR cc_start: 0.8514 (m-80) cc_final: 0.8310 (m-80) REVERT: C 29 GLU cc_start: 0.8116 (mp0) cc_final: 0.7851 (mp0) REVERT: H 47 TRP cc_start: 0.8838 (t60) cc_final: 0.8534 (t60) REVERT: H 61 ASP cc_start: 0.7857 (m-30) cc_final: 0.7630 (m-30) REVERT: L 60 PHE cc_start: 0.6118 (p90) cc_final: 0.5839 (p90) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1938 time to fit residues: 36.7285 Evaluate side-chains 119 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 4933 Z= 0.267 Angle : 0.742 11.419 6693 Z= 0.375 Chirality : 0.046 0.208 725 Planarity : 0.005 0.062 857 Dihedral : 5.180 32.923 712 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.49 % Allowed : 21.12 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.97 (0.34), residues: 604 helix: 1.07 (0.61), residues: 77 sheet: 1.12 (0.33), residues: 230 loop : 0.24 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 35 HIS 0.005 0.001 HIS L 29 PHE 0.016 0.002 PHE H 107 TYR 0.019 0.002 TYR L 85 ARG 0.004 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7959 (tm130) cc_final: 0.7693 (tm130) REVERT: A 16 GLN cc_start: 0.7757 (mm110) cc_final: 0.7037 (mm110) REVERT: A 102 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8193 (tm-30) REVERT: L 60 PHE cc_start: 0.6461 (p90) cc_final: 0.6208 (p90) outliers start: 18 outliers final: 11 residues processed: 140 average time/residue: 0.1574 time to fit residues: 28.0926 Evaluate side-chains 121 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4933 Z= 0.235 Angle : 0.701 10.671 6693 Z= 0.347 Chirality : 0.044 0.170 725 Planarity : 0.004 0.047 857 Dihedral : 4.867 30.214 712 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.26 % Allowed : 21.90 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.95 (0.34), residues: 604 helix: 0.87 (0.60), residues: 77 sheet: 1.33 (0.33), residues: 220 loop : 0.12 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 35 HIS 0.004 0.001 HIS L 29 PHE 0.016 0.002 PHE C 91 TYR 0.018 0.002 TYR L 85 ARG 0.009 0.001 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7747 (mm110) cc_final: 0.7195 (mm-40) REVERT: A 56 ASP cc_start: 0.8417 (p0) cc_final: 0.7775 (p0) REVERT: A 102 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8286 (tm-30) REVERT: A 105 PHE cc_start: 0.8188 (p90) cc_final: 0.7932 (p90) REVERT: B 61 ARG cc_start: 0.7740 (ptt180) cc_final: 0.7502 (ptt180) REVERT: H 84 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8536 (mm-30) outliers start: 22 outliers final: 16 residues processed: 140 average time/residue: 0.1517 time to fit residues: 27.6976 Evaluate side-chains 131 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.0030 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.0270 chunk 56 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 overall best weight: 0.3848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4933 Z= 0.194 Angle : 0.684 10.435 6693 Z= 0.332 Chirality : 0.044 0.202 725 Planarity : 0.004 0.039 857 Dihedral : 4.744 28.918 712 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.07 % Allowed : 22.48 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.92 (0.34), residues: 604 helix: 0.89 (0.60), residues: 77 sheet: 1.29 (0.33), residues: 224 loop : 0.08 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 35 HIS 0.004 0.001 HIS L 29 PHE 0.015 0.002 PHE L 60 TYR 0.018 0.002 TYR L 85 ARG 0.002 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7161 (tm-30) REVERT: A 56 ASP cc_start: 0.8408 (p0) cc_final: 0.7646 (p0) REVERT: A 102 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8295 (tm-30) REVERT: A 105 PHE cc_start: 0.8117 (p90) cc_final: 0.7914 (p90) REVERT: B 61 ARG cc_start: 0.7751 (ptt180) cc_final: 0.7520 (ptt180) REVERT: B 83 PHE cc_start: 0.7613 (m-80) cc_final: 0.7355 (m-80) REVERT: B 87 TYR cc_start: 0.8176 (m-80) cc_final: 0.7921 (m-80) REVERT: H 84 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8665 (mm-30) REVERT: L 60 PHE cc_start: 0.6372 (p90) cc_final: 0.6080 (p90) REVERT: L 61 SER cc_start: 0.7394 (OUTLIER) cc_final: 0.6649 (p) outliers start: 21 outliers final: 16 residues processed: 135 average time/residue: 0.1546 time to fit residues: 26.8703 Evaluate side-chains 135 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4933 Z= 0.300 Angle : 0.684 10.377 6693 Z= 0.342 Chirality : 0.044 0.168 725 Planarity : 0.004 0.039 857 Dihedral : 4.924 28.738 712 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.43 % Allowed : 21.90 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.80 (0.34), residues: 604 helix: 0.94 (0.61), residues: 77 sheet: 1.29 (0.35), residues: 205 loop : -0.02 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 35 HIS 0.006 0.002 HIS L 29 PHE 0.019 0.003 PHE C 117 TYR 0.017 0.002 TYR L 85 ARG 0.006 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 PHE cc_start: 0.7589 (m-80) cc_final: 0.7367 (m-80) REVERT: B 87 TYR cc_start: 0.8392 (m-80) cc_final: 0.7999 (m-80) outliers start: 28 outliers final: 20 residues processed: 136 average time/residue: 0.1534 time to fit residues: 27.3143 Evaluate side-chains 132 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 117 TYR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.0070 chunk 54 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN C 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4933 Z= 0.199 Angle : 0.668 10.785 6693 Z= 0.325 Chirality : 0.043 0.163 725 Planarity : 0.004 0.037 857 Dihedral : 4.757 26.840 712 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.84 % Allowed : 24.81 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.80 (0.34), residues: 604 helix: 0.97 (0.61), residues: 77 sheet: 1.24 (0.33), residues: 218 loop : -0.05 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 35 HIS 0.005 0.001 HIS L 29 PHE 0.015 0.002 PHE A 81 TYR 0.020 0.002 TYR L 85 ARG 0.002 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 PHE cc_start: 0.7614 (m-80) cc_final: 0.7353 (m-80) REVERT: B 87 TYR cc_start: 0.8287 (m-80) cc_final: 0.7982 (m-80) outliers start: 25 outliers final: 19 residues processed: 133 average time/residue: 0.1416 time to fit residues: 24.9033 Evaluate side-chains 128 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.0770 chunk 47 optimal weight: 0.0060 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.0050 chunk 22 optimal weight: 0.0770 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.1326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4933 Z= 0.175 Angle : 0.674 10.460 6693 Z= 0.329 Chirality : 0.043 0.159 725 Planarity : 0.004 0.035 857 Dihedral : 4.550 25.684 712 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.65 % Allowed : 25.19 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.88 (0.34), residues: 604 helix: 0.97 (0.62), residues: 77 sheet: 1.24 (0.33), residues: 224 loop : 0.04 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 35 HIS 0.003 0.001 HIS L 29 PHE 0.012 0.002 PHE A 105 TYR 0.019 0.001 TYR L 85 ARG 0.002 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8136 (p90) cc_final: 0.7932 (p90) REVERT: B 83 PHE cc_start: 0.7618 (m-80) cc_final: 0.7349 (m-80) REVERT: L 60 PHE cc_start: 0.6532 (p90) cc_final: 0.6120 (p90) REVERT: L 61 SER cc_start: 0.7255 (t) cc_final: 0.6640 (p) outliers start: 24 outliers final: 22 residues processed: 128 average time/residue: 0.1588 time to fit residues: 26.5257 Evaluate side-chains 132 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 117 TYR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain L residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.2980 chunk 5 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4933 Z= 0.187 Angle : 0.657 9.843 6693 Z= 0.321 Chirality : 0.043 0.168 725 Planarity : 0.004 0.035 857 Dihedral : 4.527 24.446 712 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.04 % Allowed : 25.39 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.87 (0.34), residues: 604 helix: 0.92 (0.61), residues: 77 sheet: 1.26 (0.32), residues: 224 loop : 0.04 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 35 HIS 0.003 0.001 HIS L 29 PHE 0.012 0.002 PHE H 107 TYR 0.020 0.002 TYR B 87 ARG 0.002 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 105 PHE cc_start: 0.8146 (p90) cc_final: 0.7940 (p90) REVERT: L 60 PHE cc_start: 0.6564 (p90) cc_final: 0.6191 (p90) outliers start: 26 outliers final: 22 residues processed: 133 average time/residue: 0.1433 time to fit residues: 24.8297 Evaluate side-chains 133 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 117 TYR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 0.0670 chunk 46 optimal weight: 0.2980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4933 Z= 0.193 Angle : 0.671 9.764 6693 Z= 0.328 Chirality : 0.043 0.163 725 Planarity : 0.004 0.035 857 Dihedral : 4.562 24.058 712 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.65 % Allowed : 26.36 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.83 (0.34), residues: 604 helix: 0.90 (0.61), residues: 77 sheet: 1.29 (0.33), residues: 225 loop : -0.07 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 35 HIS 0.003 0.001 HIS L 29 PHE 0.017 0.002 PHE A 81 TYR 0.028 0.002 TYR B 87 ARG 0.001 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8160 (tm-30) REVERT: A 105 PHE cc_start: 0.8139 (p90) cc_final: 0.7904 (p90) outliers start: 24 outliers final: 20 residues processed: 127 average time/residue: 0.1411 time to fit residues: 23.6359 Evaluate side-chains 128 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 117 TYR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4933 Z= 0.316 Angle : 0.727 10.660 6693 Z= 0.362 Chirality : 0.044 0.168 725 Planarity : 0.004 0.036 857 Dihedral : 5.080 25.009 712 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.14 % Favored : 95.70 % Rotamer: Outliers : 4.84 % Allowed : 26.94 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.54 (0.34), residues: 604 helix: 0.80 (0.59), residues: 77 sheet: 1.10 (0.33), residues: 220 loop : -0.27 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 35 HIS 0.005 0.002 HIS L 29 PHE 0.020 0.003 PHE C 117 TYR 0.030 0.002 TYR L 85 ARG 0.003 0.000 ARG C 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6715 (tppt) REVERT: A 79 GLN cc_start: 0.7399 (mm-40) cc_final: 0.7161 (mm110) REVERT: A 102 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8249 (tm-30) outliers start: 25 outliers final: 22 residues processed: 122 average time/residue: 0.1475 time to fit residues: 23.3322 Evaluate side-chains 128 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 117 TYR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.5878 > 50: distance: 1 - 90: 3.378 distance: 12 - 14: 18.102 distance: 14 - 15: 10.585 distance: 15 - 16: 4.879 distance: 15 - 18: 5.197 distance: 18 - 19: 5.774 distance: 18 - 20: 6.227 distance: 22 - 23: 12.685 distance: 22 - 171: 8.774 distance: 23 - 24: 10.759 distance: 23 - 26: 9.168 distance: 24 - 25: 16.532 distance: 24 - 30: 33.298 distance: 26 - 27: 8.702 distance: 27 - 28: 4.273 distance: 30 - 31: 55.588 distance: 31 - 32: 24.659 distance: 31 - 34: 42.797 distance: 32 - 33: 26.793 distance: 32 - 39: 25.339 distance: 34 - 35: 39.986 distance: 35 - 36: 51.396 distance: 36 - 37: 48.084 distance: 36 - 38: 47.580 distance: 39 - 40: 20.222 distance: 39 - 45: 33.201 distance: 40 - 41: 17.398 distance: 40 - 43: 23.892 distance: 41 - 42: 10.357 distance: 41 - 46: 3.536 distance: 43 - 44: 28.254 distance: 44 - 45: 30.852 distance: 46 - 47: 26.452 distance: 47 - 48: 29.692 distance: 47 - 50: 16.090 distance: 48 - 49: 26.056 distance: 48 - 52: 27.960 distance: 50 - 51: 7.650 distance: 52 - 53: 6.516 distance: 53 - 54: 5.750 distance: 53 - 56: 8.903 distance: 54 - 55: 18.062 distance: 54 - 61: 6.065 distance: 56 - 57: 5.986 distance: 57 - 58: 5.434 distance: 61 - 62: 21.086 distance: 62 - 63: 5.534 distance: 62 - 65: 11.377 distance: 63 - 64: 12.539 distance: 63 - 68: 21.559 distance: 65 - 66: 12.028 distance: 65 - 67: 8.608 distance: 68 - 69: 5.974 distance: 68 - 131: 5.774 distance: 69 - 72: 8.354 distance: 70 - 71: 3.577 distance: 70 - 76: 24.041 distance: 71 - 128: 15.088 distance: 72 - 73: 11.614 distance: 73 - 74: 4.943 distance: 76 - 77: 8.124 distance: 77 - 78: 8.495 distance: 77 - 80: 7.190 distance: 78 - 79: 19.441 distance: 78 - 82: 26.265 distance: 80 - 81: 15.307 distance: 82 - 83: 9.922 distance: 82 - 115: 22.239 distance: 83 - 84: 35.237 distance: 83 - 86: 34.388 distance: 84 - 85: 27.657 distance: 84 - 90: 30.848 distance: 85 - 112: 23.779 distance: 86 - 87: 17.272 distance: 87 - 88: 14.978 distance: 87 - 89: 10.264 distance: 97 - 103: 3.159