Starting phenix.real_space_refine on Fri Feb 14 12:01:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q85_18247/02_2025/8q85_18247.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q85_18247/02_2025/8q85_18247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q85_18247/02_2025/8q85_18247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q85_18247/02_2025/8q85_18247.map" model { file = "/net/cci-nas-00/data/ceres_data/8q85_18247/02_2025/8q85_18247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q85_18247/02_2025/8q85_18247.cif" } resolution = 3.97 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 6366 2.51 5 N 1836 2.21 5 O 2056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10299 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1145 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 1, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 744 Unresolved non-hydrogen angles: 925 Unresolved non-hydrogen dihedrals: 593 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 18, 'ASP:plan': 14, 'PHE:plan': 5, 'GLU:plan': 26, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 374 Chain: "G" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 886 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 173} Link IDs: {'PTRANS': 1, 'TRANS': 176} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 588 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 460 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 13, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 23, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 292 Chain: "U" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "V" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 935 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain: "W" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 837 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "X" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 535 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "Y" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "Z" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "a" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1925 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Chain breaks: 1 Chain: "b" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 561 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "c" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "d" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 859 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Time building chain proxies: 6.07, per 1000 atoms: 0.59 Number of scatterers: 10299 At special positions: 0 Unit cell: (203.52, 142.04, 216.24, 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 41 16.00 O 2056 8.00 N 1836 7.00 C 6366 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: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 86.6% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'F' and resid 434 through 478 Processing helix chain 'F' and resid 484 through 489 removed outlier: 3.688A pdb=" N LEU F 488 " --> pdb=" O ASN F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 511 removed outlier: 3.776A pdb=" N LEU F 510 " --> pdb=" O SER F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 663 Processing helix chain 'G' and resid 271 through 307 Processing helix chain 'G' and resid 307 through 337 Processing helix chain 'G' and resid 339 through 386 Processing helix chain 'G' and resid 386 through 400 Processing helix chain 'G' and resid 405 through 446 Processing helix chain 'U' and resid 58 through 110 Proline residue: U 65 - end of helix Processing helix chain 'U' and resid 120 through 151 Processing helix chain 'V' and resid 61 through 125 removed outlier: 4.618A pdb=" N LEU V 89 " --> pdb=" O LEU V 85 " (cutoff:3.500A) Proline residue: V 90 - end of helix Processing helix chain 'V' and resid 126 through 143 removed outlier: 3.670A pdb=" N LEU V 130 " --> pdb=" O ASP V 126 " (cutoff:3.500A) Processing helix chain 'V' and resid 146 through 150 Processing helix chain 'V' and resid 151 through 176 Processing helix chain 'W' and resid 3 through 67 removed outlier: 4.104A pdb=" N GLN W 7 " --> pdb=" O SER W 3 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASN W 55 " --> pdb=" O GLN W 51 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TRP W 56 " --> pdb=" O LEU W 52 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP W 57 " --> pdb=" O MET W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 73 Processing helix chain 'W' and resid 74 through 78 Processing helix chain 'W' and resid 80 through 84 Processing helix chain 'X' and resid 14 through 57 Processing helix chain 'X' and resid 58 through 67 removed outlier: 3.897A pdb=" N VAL X 62 " --> pdb=" O GLU X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 80 removed outlier: 4.066A pdb=" N ASP X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA X 80 " --> pdb=" O LEU X 76 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 41 removed outlier: 4.189A pdb=" N VAL Y 8 " --> pdb=" O PRO Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 65 removed outlier: 4.030A pdb=" N GLU Y 45 " --> pdb=" O ASN Y 41 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE Y 46 " --> pdb=" O LYS Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 6 through 35 Processing helix chain 'Z' and resid 53 through 65 removed outlier: 3.523A pdb=" N ASP Z 59 " --> pdb=" O GLN Z 55 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS Z 63 " --> pdb=" O ASP Z 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 94 removed outlier: 3.509A pdb=" N LYS Z 72 " --> pdb=" O GLY Z 68 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL Z 75 " --> pdb=" O LEU Z 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 22 Processing helix chain 'a' and resid 28 through 37 removed outlier: 3.941A pdb=" N ASN a 32 " --> pdb=" O GLY a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 40 through 51 Processing helix chain 'a' and resid 56 through 63 Processing helix chain 'a' and resid 81 through 99 Processing helix chain 'a' and resid 111 through 125 removed outlier: 3.570A pdb=" N TYR a 115 " --> pdb=" O PRO a 111 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS a 118 " --> pdb=" O VAL a 114 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU a 121 " --> pdb=" O ASN a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 168 Processing helix chain 'a' and resid 171 through 183 Processing helix chain 'a' and resid 203 through 205 No H-bonds generated for 'chain 'a' and resid 203 through 205' Processing helix chain 'a' and resid 206 through 221 removed outlier: 3.516A pdb=" N ILE a 210 " --> pdb=" O PRO a 206 " (cutoff:3.500A) Processing helix chain 'a' and resid 223 through 265 removed outlier: 4.068A pdb=" N SER a 242 " --> pdb=" O GLU a 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 38 Processing helix chain 'b' and resid 38 through 57 removed outlier: 3.512A pdb=" N THR b 57 " --> pdb=" O ILE b 53 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 69 removed outlier: 3.532A pdb=" N GLY b 61 " --> pdb=" O THR b 57 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR b 67 " --> pdb=" O MET b 63 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 40 Processing helix chain 'c' and resid 44 through 63 Processing helix chain 'd' and resid 2 through 40 Proline residue: d 32 - end of helix removed outlier: 3.676A pdb=" N THR d 39 " --> pdb=" O ASN d 35 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET d 40 " --> pdb=" O LEU d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 65 Processing helix chain 'd' and resid 65 through 108 Processing sheet with id=AA1, first strand: chain 'U' and resid 112 through 113 Processing sheet with id=AA2, first strand: chain 'a' and resid 52 through 54 Processing sheet with id=AA3, first strand: chain 'a' and resid 64 through 67 Processing sheet with id=AA4, first strand: chain 'a' and resid 185 through 189 1042 hydrogen bonds defined for protein. 3102 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: 3.20 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3628 1.34 - 1.46: 1787 1.46 - 1.58: 4905 1.58 - 1.70: 1 1.70 - 1.82: 73 Bond restraints: 10394 Sorted by residual: bond pdb=" CB PRO Z 7 " pdb=" CG PRO Z 7 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.56e+00 bond pdb=" CG GLU b 16 " pdb=" CD GLU b 16 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.30e+00 bond pdb=" CB ILE a 247 " pdb=" CG2 ILE a 247 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" CB ASP b 25 " pdb=" CG ASP b 25 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.70e+00 bond pdb=" CG ASP Z 22 " pdb=" OD1 ASP Z 22 " ideal model delta sigma weight residual 1.249 1.225 0.024 1.90e-02 2.77e+03 1.63e+00 ... (remaining 10389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 13949 3.49 - 6.99: 116 6.99 - 10.48: 23 10.48 - 13.98: 8 13.98 - 17.47: 2 Bond angle restraints: 14098 Sorted by residual: angle pdb=" CA PRO Z 7 " pdb=" N PRO Z 7 " pdb=" CD PRO Z 7 " ideal model delta sigma weight residual 112.00 100.33 11.67 1.40e+00 5.10e-01 6.95e+01 angle pdb=" CA GLU Z 85 " pdb=" CB GLU Z 85 " pdb=" CG GLU Z 85 " ideal model delta sigma weight residual 114.10 125.15 -11.05 2.00e+00 2.50e-01 3.05e+01 angle pdb=" CA LYS Z 17 " pdb=" CB LYS Z 17 " pdb=" CG LYS Z 17 " ideal model delta sigma weight residual 114.10 124.41 -10.31 2.00e+00 2.50e-01 2.66e+01 angle pdb=" CA LEU Z 23 " pdb=" CB LEU Z 23 " pdb=" CG LEU Z 23 " ideal model delta sigma weight residual 116.30 133.77 -17.47 3.50e+00 8.16e-02 2.49e+01 angle pdb=" CA MET V 77 " pdb=" CB MET V 77 " pdb=" CG MET V 77 " ideal model delta sigma weight residual 114.10 123.75 -9.65 2.00e+00 2.50e-01 2.33e+01 ... (remaining 14093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5609 17.88 - 35.76: 618 35.76 - 53.63: 142 53.63 - 71.51: 38 71.51 - 89.39: 20 Dihedral angle restraints: 6427 sinusoidal: 2201 harmonic: 4226 Sorted by residual: dihedral pdb=" CA PHE a 64 " pdb=" C PHE a 64 " pdb=" N LYS a 65 " pdb=" CA LYS a 65 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ILE Z 53 " pdb=" C ILE Z 53 " pdb=" N LEU Z 54 " pdb=" CA LEU Z 54 " ideal model delta harmonic sigma weight residual -180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PRO Z 7 " pdb=" C PRO Z 7 " pdb=" N LEU Z 8 " pdb=" CA LEU Z 8 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1640 0.106 - 0.213: 54 0.213 - 0.319: 1 0.319 - 0.426: 1 0.426 - 0.532: 1 Chirality restraints: 1697 Sorted by residual: chirality pdb=" CG LEU Z 23 " pdb=" CB LEU Z 23 " pdb=" CD1 LEU Z 23 " pdb=" CD2 LEU Z 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" CA PRO Z 7 " pdb=" N PRO Z 7 " pdb=" C PRO Z 7 " pdb=" CB PRO Z 7 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB THR V 82 " pdb=" CA THR V 82 " pdb=" OG1 THR V 82 " pdb=" CG2 THR V 82 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1694 not shown) Planarity restraints: 1868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER Z 6 " 0.087 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO Z 7 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO Z 7 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO Z 7 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP a 221 " 0.079 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO a 222 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO a 222 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO a 222 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Y 69 " -0.047 5.00e-02 4.00e+02 6.97e-02 7.76e+00 pdb=" N PRO Y 70 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO Y 70 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 70 " -0.038 5.00e-02 4.00e+02 ... (remaining 1865 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 346 2.70 - 3.25: 11884 3.25 - 3.80: 18387 3.80 - 4.35: 20876 4.35 - 4.90: 33178 Nonbonded interactions: 84671 Sorted by model distance: nonbonded pdb=" OG SER W 3 " pdb=" OD1 ASP W 5 " model vdw 2.146 3.040 nonbonded pdb=" O ALA a 15 " pdb=" OG SER a 18 " model vdw 2.159 3.040 nonbonded pdb=" O LYS V 73 " pdb=" NZ LYS V 73 " model vdw 2.170 3.120 nonbonded pdb=" O LEU G 336 " pdb=" N MET G 341 " model vdw 2.186 3.120 nonbonded pdb=" O LEU V 64 " pdb=" OG SER V 68 " model vdw 2.192 3.040 ... (remaining 84666 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: 0.00 ========== 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=0.00 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: 2.210 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.180 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 0.128 10394 Z= 0.259 Angle : 0.923 17.470 14098 Z= 0.491 Chirality : 0.047 0.532 1697 Planarity : 0.007 0.123 1868 Dihedral : 17.196 89.389 3651 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.53 % Allowed : 31.30 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.93 (0.22), residues: 1408 helix: 1.67 (0.14), residues: 1181 sheet: -2.04 (1.08), residues: 12 loop : -0.54 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 59 HIS 0.006 0.001 HIS a 31 PHE 0.026 0.002 PHE a 83 TYR 0.028 0.002 TYR a 230 ARG 0.007 0.001 ARG d 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 234 time to evaluate : 1.120 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 34 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8038 (mm-30) REVERT: W 79 GLU cc_start: 0.8083 (mp0) cc_final: 0.7725 (pm20) REVERT: Y 1 MET cc_start: 0.3898 (OUTLIER) cc_final: 0.3238 (mmt) REVERT: Z 11 GLU cc_start: 0.9588 (tm-30) cc_final: 0.9220 (pp20) REVERT: Z 38 HIS cc_start: 0.6533 (p-80) cc_final: 0.5048 (p-80) REVERT: a 230 TYR cc_start: 0.8856 (t80) cc_final: 0.8228 (t80) REVERT: d 67 GLU cc_start: 0.8602 (tp30) cc_final: 0.8346 (tp30) outliers start: 5 outliers final: 1 residues processed: 235 average time/residue: 0.2620 time to fit residues: 83.4929 Evaluate side-chains 223 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain Y residue 1 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 50.0000 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 125 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 108 ASN ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 ASN Z 41 GLN a 239 GLN c 63 GLN d 30 ASN d 92 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.146233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.105516 restraints weight = 32663.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.108140 restraints weight = 19049.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.109804 restraints weight = 13323.240| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10394 Z= 0.201 Angle : 0.686 12.345 14098 Z= 0.350 Chirality : 0.042 0.475 1697 Planarity : 0.004 0.079 1868 Dihedral : 4.735 55.294 1503 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.41 % Allowed : 23.63 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.22), residues: 1408 helix: 2.48 (0.14), residues: 1184 sheet: -2.00 (1.03), residues: 12 loop : -0.45 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 PHE 0.021 0.002 PHE X 20 TYR 0.020 0.002 TYR a 230 ARG 0.004 0.001 ARG d 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 1.157 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8014 (tm-30) REVERT: U 93 ASP cc_start: 0.8078 (m-30) cc_final: 0.7820 (m-30) REVERT: U 120 ASP cc_start: 0.7931 (p0) cc_final: 0.7724 (p0) REVERT: W 11 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8192 (mtpt) REVERT: W 34 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8192 (mm-30) REVERT: W 72 GLN cc_start: 0.8292 (tp40) cc_final: 0.8012 (tp-100) REVERT: W 75 GLU cc_start: 0.8425 (tp30) cc_final: 0.8222 (tm-30) REVERT: W 79 GLU cc_start: 0.8115 (mp0) cc_final: 0.7756 (pm20) REVERT: Z 16 TYR cc_start: 0.7888 (m-80) cc_final: 0.6696 (m-80) REVERT: Z 17 LYS cc_start: 0.9553 (mmtt) cc_final: 0.9175 (mmtt) REVERT: Z 38 HIS cc_start: 0.5676 (p-80) cc_final: 0.4352 (p-80) REVERT: a 93 MET cc_start: 0.7454 (mmt) cc_final: 0.6991 (mmm) REVERT: a 168 PHE cc_start: 0.7606 (m-80) cc_final: 0.6409 (m-80) REVERT: a 227 LYS cc_start: 0.9272 (mmmt) cc_final: 0.8959 (mmmt) REVERT: b 1 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6744 (ppp) REVERT: b 48 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8214 (tm-30) REVERT: d 63 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8942 (tp) REVERT: d 67 GLU cc_start: 0.8491 (tp30) cc_final: 0.8108 (tp30) outliers start: 42 outliers final: 15 residues processed: 271 average time/residue: 0.2433 time to fit residues: 90.2322 Evaluate side-chains 244 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 118 VAL Chi-restraints excluded: chain W residue 122 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Y residue 51 CYS Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain d residue 63 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 129 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 60.0000 chunk 61 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 55 HIS ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.146391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.104225 restraints weight = 33601.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.106737 restraints weight = 20143.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.108351 restraints weight = 14386.432| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10394 Z= 0.202 Angle : 0.667 12.951 14098 Z= 0.335 Chirality : 0.040 0.240 1697 Planarity : 0.004 0.061 1868 Dihedral : 4.543 55.976 1500 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.05 % Allowed : 24.05 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.22), residues: 1408 helix: 2.74 (0.14), residues: 1171 sheet: -2.08 (1.04), residues: 12 loop : -0.56 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 PHE 0.018 0.002 PHE X 20 TYR 0.022 0.002 TYR a 230 ARG 0.006 0.001 ARG d 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 1.290 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7958 (tm-30) REVERT: U 93 ASP cc_start: 0.8057 (m-30) cc_final: 0.7712 (m-30) REVERT: U 98 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8465 (mm) REVERT: W 6 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7858 (pt0) REVERT: W 34 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8189 (mm-30) REVERT: W 72 GLN cc_start: 0.8274 (tp40) cc_final: 0.8044 (tp-100) REVERT: W 79 GLU cc_start: 0.8107 (mp0) cc_final: 0.7706 (pm20) REVERT: X 47 ILE cc_start: 0.7621 (mt) cc_final: 0.7386 (mm) REVERT: Z 16 TYR cc_start: 0.7691 (m-80) cc_final: 0.6410 (m-80) REVERT: Z 17 LYS cc_start: 0.9613 (mmtt) cc_final: 0.9272 (mmtt) REVERT: Z 22 ASP cc_start: 0.8231 (t0) cc_final: 0.7724 (p0) REVERT: Z 38 HIS cc_start: 0.5792 (p-80) cc_final: 0.4249 (p-80) REVERT: a 188 MET cc_start: 0.3787 (ppp) cc_final: 0.3543 (ppp) REVERT: a 227 LYS cc_start: 0.9139 (mmmt) cc_final: 0.8894 (mmmt) REVERT: a 230 TYR cc_start: 0.8711 (t80) cc_final: 0.8045 (t80) REVERT: a 259 LYS cc_start: 0.9368 (mmmt) cc_final: 0.9028 (mtmm) REVERT: b 1 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.6718 (ppp) REVERT: c 38 ASN cc_start: 0.8460 (m-40) cc_final: 0.8242 (m110) REVERT: d 63 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8990 (tp) REVERT: d 67 GLU cc_start: 0.8521 (tp30) cc_final: 0.8125 (tp30) outliers start: 29 outliers final: 17 residues processed: 259 average time/residue: 0.2485 time to fit residues: 88.3286 Evaluate side-chains 248 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 81 PHE Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 118 VAL Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 16 GLU Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 126 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 7 optimal weight: 50.0000 chunk 132 optimal weight: 0.0370 chunk 68 optimal weight: 0.1980 chunk 92 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 109 HIS ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.146912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.106962 restraints weight = 31793.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.109534 restraints weight = 18368.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.111167 restraints weight = 12782.309| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10394 Z= 0.176 Angle : 0.657 13.182 14098 Z= 0.330 Chirality : 0.040 0.425 1697 Planarity : 0.004 0.051 1868 Dihedral : 4.470 55.292 1500 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.47 % Allowed : 24.58 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.22), residues: 1408 helix: 2.82 (0.14), residues: 1183 sheet: -1.91 (1.06), residues: 12 loop : -0.36 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 PHE 0.017 0.002 PHE X 20 TYR 0.020 0.001 TYR a 230 ARG 0.006 0.000 ARG d 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 257 time to evaluate : 1.274 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 78 ASP cc_start: 0.7690 (t0) cc_final: 0.7406 (t0) REVERT: U 83 ARG cc_start: 0.7644 (ptp-170) cc_final: 0.7388 (ptp-170) REVERT: U 89 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8125 (tm-30) REVERT: U 93 ASP cc_start: 0.8189 (m-30) cc_final: 0.7808 (m-30) REVERT: U 94 LEU cc_start: 0.8972 (tp) cc_final: 0.8728 (tt) REVERT: U 98 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8378 (mm) REVERT: V 77 MET cc_start: 0.9112 (ppp) cc_final: 0.8838 (ppp) REVERT: W 6 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7847 (pt0) REVERT: W 34 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8186 (mm-30) REVERT: W 79 GLU cc_start: 0.8034 (mp0) cc_final: 0.7624 (pm20) REVERT: X 47 ILE cc_start: 0.7592 (mt) cc_final: 0.7389 (mm) REVERT: Z 16 TYR cc_start: 0.7664 (m-80) cc_final: 0.6281 (m-80) REVERT: Z 17 LYS cc_start: 0.9595 (mmtt) cc_final: 0.9252 (mmtt) REVERT: Z 24 LYS cc_start: 0.8752 (mttp) cc_final: 0.8356 (mttp) REVERT: Z 35 TYR cc_start: 0.5919 (t80) cc_final: 0.5708 (t80) REVERT: Z 38 HIS cc_start: 0.5734 (p-80) cc_final: 0.4661 (p-80) REVERT: a 168 PHE cc_start: 0.7357 (m-80) cc_final: 0.6800 (m-80) REVERT: a 188 MET cc_start: 0.4216 (ppp) cc_final: 0.3265 (ppp) REVERT: a 227 LYS cc_start: 0.9239 (mmmt) cc_final: 0.8986 (mmmt) REVERT: a 230 TYR cc_start: 0.8618 (t80) cc_final: 0.8168 (t80) REVERT: b 1 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6505 (ppp) REVERT: b 48 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8236 (tm-30) REVERT: b 51 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7351 (tm-30) REVERT: c 1 MET cc_start: 0.7828 (tmm) cc_final: 0.7537 (tmm) REVERT: c 6 GLN cc_start: 0.7963 (tm130) cc_final: 0.7468 (tm-30) REVERT: c 9 TYR cc_start: 0.8794 (m-80) cc_final: 0.8589 (m-80) REVERT: d 63 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8967 (tp) REVERT: d 67 GLU cc_start: 0.8492 (tp30) cc_final: 0.8084 (tp30) REVERT: d 89 ASP cc_start: 0.9138 (t0) cc_final: 0.8858 (m-30) outliers start: 33 outliers final: 21 residues processed: 275 average time/residue: 0.2572 time to fit residues: 95.9098 Evaluate side-chains 260 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 81 PHE Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain U residue 135 GLU Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 118 VAL Chi-restraints excluded: chain X residue 58 GLU Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Y residue 51 CYS Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain d residue 2 THR Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 25 optimal weight: 60.0000 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.146621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.105106 restraints weight = 32313.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.107634 restraints weight = 18988.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.109194 restraints weight = 13369.038| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10394 Z= 0.195 Angle : 0.680 13.313 14098 Z= 0.343 Chirality : 0.041 0.355 1697 Planarity : 0.004 0.048 1868 Dihedral : 4.439 56.469 1500 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.52 % Allowed : 25.84 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.22), residues: 1408 helix: 2.83 (0.14), residues: 1182 sheet: -2.06 (1.09), residues: 12 loop : -0.36 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 59 HIS 0.014 0.001 HIS a 109 PHE 0.014 0.002 PHE X 20 TYR 0.017 0.001 TYR a 230 ARG 0.009 0.001 ARG d 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 1.184 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8145 (tm-30) REVERT: U 93 ASP cc_start: 0.8187 (m-30) cc_final: 0.7818 (m-30) REVERT: U 94 LEU cc_start: 0.8990 (tp) cc_final: 0.8743 (tt) REVERT: U 98 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8375 (mm) REVERT: V 79 LYS cc_start: 0.9381 (mmmt) cc_final: 0.9158 (mmmt) REVERT: W 6 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7850 (pt0) REVERT: W 34 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8187 (mm-30) REVERT: W 79 GLU cc_start: 0.7971 (mp0) cc_final: 0.7557 (pm20) REVERT: X 43 ASN cc_start: 0.7860 (m-40) cc_final: 0.7594 (m-40) REVERT: Z 16 TYR cc_start: 0.7732 (m-80) cc_final: 0.6379 (m-80) REVERT: Z 17 LYS cc_start: 0.9620 (mmtt) cc_final: 0.9308 (mmtt) REVERT: Z 21 LEU cc_start: 0.9113 (pp) cc_final: 0.8772 (pp) REVERT: Z 22 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7042 (m-30) REVERT: Z 24 LYS cc_start: 0.8744 (mttp) cc_final: 0.8326 (mttp) REVERT: Z 38 HIS cc_start: 0.5717 (p-80) cc_final: 0.4715 (p-80) REVERT: a 188 MET cc_start: 0.4179 (ppp) cc_final: 0.3744 (ppp) REVERT: a 227 LYS cc_start: 0.9238 (mmmt) cc_final: 0.8989 (mmmt) REVERT: a 230 TYR cc_start: 0.8613 (t80) cc_final: 0.8126 (t80) REVERT: b 1 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6515 (ppp) REVERT: b 48 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8244 (tm-30) REVERT: b 51 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7268 (tm-30) REVERT: c 6 GLN cc_start: 0.7947 (tm130) cc_final: 0.7471 (tm-30) REVERT: c 9 TYR cc_start: 0.8790 (m-80) cc_final: 0.8513 (m-80) REVERT: d 67 GLU cc_start: 0.8543 (tp30) cc_final: 0.8342 (tp30) REVERT: d 89 ASP cc_start: 0.9216 (t0) cc_final: 0.8982 (m-30) outliers start: 43 outliers final: 25 residues processed: 279 average time/residue: 0.2470 time to fit residues: 93.6458 Evaluate side-chains 260 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 81 PHE Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 118 VAL Chi-restraints excluded: chain W residue 122 GLU Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 58 GLU Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 51 CYS Chi-restraints excluded: chain Z residue 22 ASP Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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: 57.2882 > 50: distance: 18 - 46: 32.318 distance: 25 - 54: 28.182 distance: 32 - 63: 12.752 distance: 43 - 46: 32.662 distance: 46 - 47: 47.826 distance: 47 - 48: 24.458 distance: 47 - 50: 8.118 distance: 48 - 49: 33.060 distance: 48 - 54: 40.957 distance: 50 - 51: 43.853 distance: 51 - 52: 46.801 distance: 51 - 53: 32.927 distance: 54 - 55: 9.818 distance: 55 - 56: 21.469 distance: 55 - 58: 37.106 distance: 56 - 57: 27.214 distance: 56 - 63: 16.468 distance: 58 - 59: 18.511 distance: 59 - 60: 22.350 distance: 60 - 61: 7.607 distance: 60 - 62: 7.625 distance: 63 - 64: 10.124 distance: 64 - 65: 6.061 distance: 64 - 67: 6.281 distance: 65 - 66: 9.875 distance: 65 - 71: 16.833 distance: 67 - 68: 11.506 distance: 68 - 69: 5.767 distance: 68 - 70: 10.138 distance: 71 - 72: 8.260 distance: 72 - 73: 17.126 distance: 73 - 74: 8.280 distance: 73 - 75: 29.211 distance: 75 - 76: 20.201 distance: 76 - 77: 22.068 distance: 76 - 79: 22.033 distance: 77 - 78: 10.561 distance: 77 - 81: 53.589 distance: 79 - 80: 3.361 distance: 81 - 82: 9.372 distance: 81 - 182: 28.169 distance: 82 - 83: 33.982 distance: 82 - 85: 6.606 distance: 83 - 84: 11.808 distance: 83 - 88: 11.117 distance: 84 - 179: 21.808 distance: 85 - 86: 41.015 distance: 85 - 87: 14.879 distance: 88 - 89: 26.989 distance: 89 - 90: 17.666 distance: 89 - 92: 12.737 distance: 90 - 91: 37.874 distance: 90 - 96: 16.854 distance: 92 - 93: 30.919 distance: 93 - 94: 14.103 distance: 93 - 95: 11.814 distance: 96 - 97: 6.693 distance: 96 - 167: 16.412 distance: 97 - 98: 12.333 distance: 98 - 99: 10.063 distance: 98 - 104: 21.565 distance: 99 - 164: 10.616 distance: 100 - 101: 19.108 distance: 101 - 102: 13.258 distance: 102 - 103: 24.176 distance: 104 - 105: 30.002 distance: 105 - 106: 53.422 distance: 105 - 108: 25.567 distance: 106 - 107: 8.885 distance: 106 - 113: 41.172 distance: 108 - 109: 17.004 distance: 109 - 110: 13.088 distance: 110 - 111: 11.550 distance: 110 - 112: 9.022 distance: 113 - 114: 21.917 distance: 114 - 115: 25.972 distance: 114 - 117: 23.341 distance: 115 - 116: 19.923 distance: 115 - 122: 5.219 distance: 117 - 118: 15.394 distance: 118 - 119: 6.646 distance: 119 - 120: 6.536