Starting phenix.real_space_refine on Fri Feb 14 18:52:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u8g_26383/02_2025/7u8g_26383_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u8g_26383/02_2025/7u8g_26383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u8g_26383/02_2025/7u8g_26383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u8g_26383/02_2025/7u8g_26383.map" model { file = "/net/cci-nas-00/data/ceres_data/7u8g_26383/02_2025/7u8g_26383_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u8g_26383/02_2025/7u8g_26383_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 3 5.49 5 S 27 5.16 5 C 3292 2.51 5 N 827 2.21 5 O 895 1.98 5 H 4861 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9907 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 4247 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 248} Chain breaks: 1 Chain: "B" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2081 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "D" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1738 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1640 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 182 Unusual residues: {'HEM': 2, 'NAG': 3, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.96, per 1000 atoms: 0.60 Number of scatterers: 9907 At special positions: 0 Unit cell: (57.749, 70.907, 128.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 27 16.00 P 3 15.00 O 895 8.00 N 827 7.00 C 3292 6.00 H 4861 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS A 257 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 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=2, symmetry=0 Links applied NAG-ASN " NAG A 603 " - " ASN A 240 " " NAG A 604 " - " ASN A 149 " " NAG A 605 " - " ASN A 132 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 687.9 milliseconds 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1134 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 6 sheets defined 52.0% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 7 through 35 removed outlier: 3.779A pdb=" N SER A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'A' and resid 48 through 68 Proline residue: A 56 - end of helix removed outlier: 4.611A pdb=" N LEU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 131 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 173 through 193 Processing helix chain 'A' and resid 194 through 201 Processing helix chain 'A' and resid 201 through 210 removed outlier: 3.773A pdb=" N HIS A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.568A pdb=" N ILE A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.627A pdb=" N VAL A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.614A pdb=" N TRP A 251 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 287 removed outlier: 3.627A pdb=" N TRP A 272 " --> pdb=" O MET A 268 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'B' and resid 5 through 31 removed outlier: 4.196A pdb=" N TRP B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 12 " --> pdb=" O MET B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 54 removed outlier: 4.020A pdb=" N GLY B 39 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.478A pdb=" N MET B 73 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.601A pdb=" N ARG B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 102 removed outlier: 3.760A pdb=" N ARG B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 104 through 127 removed outlier: 4.330A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLY B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.720A pdb=" N LYS D 65 " --> pdb=" O ARG D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.679A pdb=" N ASP E 82 " --> pdb=" O GLU E 79 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 229 through 231 Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.672A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 110 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR D 99 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU D 108 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.672A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.745A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.664A pdb=" N VAL E 11 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 768 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: 3.58 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 4853 1.08 - 1.33: 893 1.33 - 1.57: 4246 1.57 - 1.82: 43 1.82 - 2.06: 8 Bond restraints: 10043 Sorted by residual: bond pdb=" O12 POV B 201 " pdb=" P POV B 201 " ideal model delta sigma weight residual 1.657 1.463 0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" C31 POV A 601 " pdb=" O31 POV A 601 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C31 POV B 201 " pdb=" O31 POV B 201 " ideal model delta sigma weight residual 1.327 1.421 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C31 POV A 602 " pdb=" O31 POV A 602 " ideal model delta sigma weight residual 1.327 1.420 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C31 POV A 602 " pdb=" C32 POV A 602 " ideal model delta sigma weight residual 1.502 1.556 -0.054 2.00e-02 2.50e+03 7.39e+00 ... (remaining 10038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.75: 18000 5.75 - 11.51: 13 11.51 - 17.26: 3 17.26 - 23.01: 2 23.01 - 28.76: 3 Bond angle restraints: 18021 Sorted by residual: angle pdb=" C34 POV A 602 " pdb=" C35 POV A 602 " pdb=" C36 POV A 602 " ideal model delta sigma weight residual 112.32 141.08 -28.76 3.00e+00 1.11e-01 9.19e+01 angle pdb=" C34 POV A 601 " pdb=" C35 POV A 601 " pdb=" C36 POV A 601 " ideal model delta sigma weight residual 112.32 140.31 -27.99 3.00e+00 1.11e-01 8.71e+01 angle pdb=" C34 POV B 201 " pdb=" C35 POV B 201 " pdb=" C36 POV B 201 " ideal model delta sigma weight residual 112.32 139.07 -26.75 3.00e+00 1.11e-01 7.95e+01 angle pdb=" O13 POV A 601 " pdb=" P POV A 601 " pdb=" O14 POV A 601 " ideal model delta sigma weight residual 121.11 100.63 20.48 3.00e+00 1.11e-01 4.66e+01 angle pdb=" O13 POV A 602 " pdb=" P POV A 602 " pdb=" O14 POV A 602 " ideal model delta sigma weight residual 121.11 101.14 19.97 3.00e+00 1.11e-01 4.43e+01 ... (remaining 18016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 4270 17.18 - 34.36: 354 34.36 - 51.55: 92 51.55 - 68.73: 41 68.73 - 85.91: 16 Dihedral angle restraints: 4773 sinusoidal: 2582 harmonic: 2191 Sorted by residual: dihedral pdb=" CA LEU A 66 " pdb=" C LEU A 66 " pdb=" N ILE A 67 " pdb=" CA ILE A 67 " ideal model delta harmonic sigma weight residual -180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" C1A HEM A 607 " pdb=" C2A HEM A 607 " pdb=" CAA HEM A 607 " pdb=" CBA HEM A 607 " ideal model delta sinusoidal sigma weight residual 0.00 79.89 -79.89 2 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" C2D HEM A 607 " pdb=" C3D HEM A 607 " pdb=" CAD HEM A 607 " pdb=" CBD HEM A 607 " ideal model delta sinusoidal sigma weight residual 180.00 104.07 75.93 2 2.00e+01 2.50e-03 1.13e+01 ... (remaining 4770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 778 0.164 - 0.327: 0 0.327 - 0.491: 0 0.491 - 0.654: 0 0.654 - 0.818: 1 Chirality restraints: 779 Sorted by residual: chirality pdb=" C5 NAG A 603 " pdb=" C4 NAG A 603 " pdb=" C6 NAG A 603 " pdb=" O5 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.41 -1.59 -0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb=" CA ILE E 48 " pdb=" N ILE E 48 " pdb=" C ILE E 48 " pdb=" CB ILE E 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA VAL E 58 " pdb=" N VAL E 58 " pdb=" C VAL E 58 " pdb=" CB VAL E 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 776 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 275 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 276 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 7 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO E 8 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO E 8 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 8 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 199 " 0.098 9.50e-02 1.11e+02 3.28e-02 1.17e+00 pdb=" NE ARG A 199 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 199 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 199 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 199 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 199 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 199 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG A 199 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 199 " 0.000 2.00e-02 2.50e+03 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 629 2.20 - 2.80: 20109 2.80 - 3.40: 27202 3.40 - 4.00: 36460 4.00 - 4.60: 56534 Nonbonded interactions: 140934 Sorted by model distance: nonbonded pdb=" OD1 ASN B 11 " pdb="HH22 ARG B 67 " model vdw 1.603 2.450 nonbonded pdb=" HH TYR A 137 " pdb=" O GLU A 245 " model vdw 1.616 2.450 nonbonded pdb=" OE1 GLN D 39 " pdb="HE22 GLN E 38 " model vdw 1.619 2.450 nonbonded pdb=" O GLY E 68 " pdb=" HH TYR E 71 " model vdw 1.636 2.450 nonbonded pdb=" O ALA B 101 " pdb=" HG1 THR B 107 " model vdw 1.637 2.450 ... (remaining 140929 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 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: 0.170 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.540 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.006 0.194 5182 Z= 0.399 Angle : 0.992 28.765 7060 Z= 0.388 Chirality : 0.049 0.818 779 Planarity : 0.004 0.049 851 Dihedral : 14.761 85.910 1862 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.96 (0.36), residues: 611 helix: 2.04 (0.33), residues: 262 sheet: 0.40 (0.55), residues: 105 loop : -0.81 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 270 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.016 0.001 TYR B 121 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.790 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.4565 time to fit residues: 36.3345 Evaluate side-chains 57 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.100837 restraints weight = 17528.998| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.72 r_work: 0.3052 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5182 Z= 0.233 Angle : 0.530 9.896 7060 Z= 0.265 Chirality : 0.040 0.147 779 Planarity : 0.004 0.047 851 Dihedral : 10.896 85.158 807 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.20 % Allowed : 4.52 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.84 (0.35), residues: 611 helix: 1.99 (0.32), residues: 263 sheet: 0.35 (0.54), residues: 105 loop : -0.97 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.003 0.001 HIS A 115 PHE 0.011 0.001 PHE D 94 TYR 0.011 0.001 TYR B 121 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.770 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.4988 time to fit residues: 37.2903 Evaluate side-chains 54 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.120634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101425 restraints weight = 17809.529| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.78 r_work: 0.3207 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5182 Z= 0.205 Angle : 0.494 8.928 7060 Z= 0.246 Chirality : 0.040 0.203 779 Planarity : 0.004 0.042 851 Dihedral : 9.942 85.649 807 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.59 % Allowed : 6.88 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 611 helix: 2.01 (0.32), residues: 264 sheet: 0.35 (0.55), residues: 105 loop : -1.09 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.003 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.010 0.001 TYR E 49 ARG 0.004 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.763 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 60 average time/residue: 0.5285 time to fit residues: 39.6192 Evaluate side-chains 58 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.102069 restraints weight = 17658.630| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.72 r_work: 0.3090 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5182 Z= 0.181 Angle : 0.469 8.656 7060 Z= 0.232 Chirality : 0.039 0.144 779 Planarity : 0.003 0.038 851 Dihedral : 9.278 86.707 807 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.79 % Allowed : 7.86 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.95 (0.35), residues: 611 helix: 2.11 (0.32), residues: 267 sheet: 0.46 (0.56), residues: 105 loop : -1.03 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.003 0.001 HIS A 115 PHE 0.008 0.001 PHE A 155 TYR 0.009 0.001 TYR E 49 ARG 0.004 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.716 Fit side-chains REVERT: D 9 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7591 (m-30) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 0.5023 time to fit residues: 39.4067 Evaluate side-chains 61 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.118617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099738 restraints weight = 17715.665| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.75 r_work: 0.3006 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5182 Z= 0.258 Angle : 0.505 10.068 7060 Z= 0.248 Chirality : 0.040 0.144 779 Planarity : 0.003 0.038 851 Dihedral : 9.336 87.440 807 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.79 % Allowed : 8.25 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.85 (0.35), residues: 611 helix: 2.05 (0.32), residues: 267 sheet: 0.45 (0.56), residues: 105 loop : -1.13 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.005 0.001 HIS A 115 PHE 0.011 0.001 PHE A 155 TYR 0.013 0.001 TYR E 49 ARG 0.006 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 1.133 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 64 average time/residue: 0.5390 time to fit residues: 41.7258 Evaluate side-chains 64 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.099991 restraints weight = 17691.397| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.76 r_work: 0.3123 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5182 Z= 0.234 Angle : 0.491 9.221 7060 Z= 0.242 Chirality : 0.039 0.144 779 Planarity : 0.003 0.036 851 Dihedral : 9.102 84.707 807 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.98 % Allowed : 8.45 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.86 (0.35), residues: 611 helix: 2.06 (0.32), residues: 267 sheet: 0.46 (0.56), residues: 105 loop : -1.15 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.012 0.001 TYR E 49 ARG 0.004 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.731 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 0.5121 time to fit residues: 40.2087 Evaluate side-chains 65 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.133626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116876 restraints weight = 17429.119| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.53 r_work: 0.2989 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5182 Z= 0.229 Angle : 0.494 9.237 7060 Z= 0.242 Chirality : 0.039 0.144 779 Planarity : 0.003 0.037 851 Dihedral : 8.716 80.043 807 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.79 % Allowed : 9.43 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.35), residues: 611 helix: 2.10 (0.32), residues: 267 sheet: 0.43 (0.56), residues: 105 loop : -1.16 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.012 0.001 TYR E 49 ARG 0.005 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.783 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 0.5142 time to fit residues: 37.5518 Evaluate side-chains 60 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.118061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.098909 restraints weight = 17962.206| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.78 r_work: 0.3074 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5182 Z= 0.254 Angle : 0.505 9.582 7060 Z= 0.248 Chirality : 0.040 0.200 779 Planarity : 0.003 0.037 851 Dihedral : 8.593 74.003 807 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.98 % Allowed : 9.04 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.35), residues: 611 helix: 2.04 (0.32), residues: 267 sheet: 0.38 (0.56), residues: 105 loop : -1.20 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.004 0.001 HIS A 239 PHE 0.010 0.001 PHE A 212 TYR 0.013 0.001 TYR E 49 ARG 0.005 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.756 Fit side-chains REVERT: A 268 MET cc_start: 0.8569 (mmt) cc_final: 0.7797 (mmt) outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 0.5204 time to fit residues: 38.3221 Evaluate side-chains 62 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.118291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.099127 restraints weight = 17783.783| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.78 r_work: 0.2995 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5182 Z= 0.235 Angle : 0.495 9.170 7060 Z= 0.244 Chirality : 0.040 0.145 779 Planarity : 0.003 0.037 851 Dihedral : 8.465 70.620 807 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.79 % Allowed : 9.23 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.79 (0.35), residues: 611 helix: 2.04 (0.32), residues: 267 sheet: 0.39 (0.56), residues: 105 loop : -1.20 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.012 0.001 TYR E 49 ARG 0.005 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.774 Fit side-chains REVERT: A 268 MET cc_start: 0.8540 (mmt) cc_final: 0.7741 (mmt) outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 0.5215 time to fit residues: 38.4339 Evaluate side-chains 59 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.099415 restraints weight = 17810.618| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.79 r_work: 0.3051 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5182 Z= 0.220 Angle : 0.490 9.038 7060 Z= 0.241 Chirality : 0.040 0.145 779 Planarity : 0.003 0.038 851 Dihedral : 8.310 67.117 807 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.79 % Allowed : 9.63 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.82 (0.35), residues: 611 helix: 2.06 (0.32), residues: 267 sheet: 0.41 (0.56), residues: 105 loop : -1.18 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.011 0.001 TYR E 49 ARG 0.006 0.000 ARG B 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.730 Fit side-chains REVERT: A 268 MET cc_start: 0.8580 (mmt) cc_final: 0.7816 (mmt) outliers start: 4 outliers final: 4 residues processed: 58 average time/residue: 0.5212 time to fit residues: 36.9009 Evaluate side-chains 59 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 0.2980 chunk 3 optimal weight: 0.0030 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.120082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.100844 restraints weight = 17702.379| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.80 r_work: 0.3020 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5182 Z= 0.184 Angle : 0.475 8.380 7060 Z= 0.234 Chirality : 0.039 0.144 779 Planarity : 0.003 0.037 851 Dihedral : 7.955 61.354 807 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.79 % Allowed : 9.63 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.91 (0.35), residues: 611 helix: 2.15 (0.32), residues: 267 sheet: 0.44 (0.56), residues: 105 loop : -1.15 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 270 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.008 0.001 TYR E 49 ARG 0.006 0.000 ARG B 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5561.39 seconds wall clock time: 98 minutes 30.67 seconds (5910.67 seconds total)