Starting phenix.real_space_refine on Tue Jan 14 21:22:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0i_45085/01_2025/9c0i_45085.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0i_45085/01_2025/9c0i_45085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c0i_45085/01_2025/9c0i_45085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0i_45085/01_2025/9c0i_45085.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0i_45085/01_2025/9c0i_45085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0i_45085/01_2025/9c0i_45085.cif" } resolution = 2.91 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= 0.004 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 K 1 8.98 5 P 197 5.49 5 Mg 1 5.21 5 S 13 5.16 5 C 4108 2.51 5 N 1355 2.21 5 O 2001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7676 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3481 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 411} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "R" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 4089 Classifications: {'RNA': 192} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 12, 'rna3p_pur': 81, 'rna3p_pyr': 81} Link IDs: {'rna2p': 30, 'rna3p': 161} Chain breaks: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.13, per 1000 atoms: 0.67 Number of scatterers: 7676 At special positions: 0 Unit cell: (130.832, 125.528, 83.096, 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) K 1 19.00 S 13 16.00 P 197 15.00 Mg 1 11.99 O 2001 8.00 N 1355 7.00 C 4108 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: 2.00 Conformation dependent library (CDL) restraints added in 431.5 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 4 sheets defined 54.4% alpha, 17.6% beta 71 base pairs and 116 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 removed outlier: 3.521A pdb=" N ASP A 5 " --> pdb=" O ASN A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.598A pdb=" N SER A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 76 through 101 removed outlier: 3.986A pdb=" N GLY A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 97 " --> pdb=" O HIS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 237 through 246 removed outlier: 3.744A pdb=" N MET A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.746A pdb=" N ARG A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 282 through 291 Processing helix chain 'A' and resid 300 through 303 removed outlier: 3.855A pdb=" N THR A 303 " --> pdb=" O THR A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 336 through 368 removed outlier: 3.765A pdb=" N LEU A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 385 Processing helix chain 'A' and resid 391 through 404 removed outlier: 3.522A pdb=" N TYR A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.850A pdb=" N LYS A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 425 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 74 removed outlier: 6.259A pdb=" N PHE A 44 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 267 removed outlier: 4.837A pdb=" N GLU A 297 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 267 removed outlier: 3.569A pdb=" N CYS A 134 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 323 197 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 172 hydrogen bonds 304 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 116 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 853 1.31 - 1.44: 3375 1.44 - 1.56: 3600 1.56 - 1.68: 385 1.68 - 1.81: 22 Bond restraints: 8235 Sorted by residual: bond pdb=" CA SER A 22 " pdb=" CB SER A 22 " ideal model delta sigma weight residual 1.532 1.465 0.067 1.59e-02 3.96e+03 1.77e+01 bond pdb=" CA ALA A 26 " pdb=" CB ALA A 26 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.55e-02 4.16e+03 1.51e+01 bond pdb=" C PRO A 20 " pdb=" O PRO A 20 " ideal model delta sigma weight residual 1.233 1.186 0.047 1.24e-02 6.50e+03 1.45e+01 bond pdb=" C PRO A 199 " pdb=" O PRO A 199 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.30e-02 5.92e+03 1.40e+01 bond pdb=" CA SER A 80 " pdb=" CB SER A 80 " ideal model delta sigma weight residual 1.528 1.475 0.054 1.66e-02 3.63e+03 1.05e+01 ... (remaining 8230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 11683 2.63 - 5.26: 315 5.26 - 7.89: 40 7.89 - 10.51: 4 10.51 - 13.14: 2 Bond angle restraints: 12044 Sorted by residual: angle pdb=" C3' A R 24 " pdb=" O3' A R 24 " pdb=" P U R 25 " ideal model delta sigma weight residual 120.20 107.06 13.14 1.50e+00 4.44e-01 7.68e+01 angle pdb=" C3' U R 23 " pdb=" O3' U R 23 " pdb=" P A R 24 " ideal model delta sigma weight residual 120.20 110.80 9.40 1.50e+00 4.44e-01 3.92e+01 angle pdb=" N ILE A 291 " pdb=" CA ILE A 291 " pdb=" C ILE A 291 " ideal model delta sigma weight residual 112.90 107.57 5.33 9.60e-01 1.09e+00 3.08e+01 angle pdb=" N ILE A 128 " pdb=" CA ILE A 128 " pdb=" C ILE A 128 " ideal model delta sigma weight residual 110.72 105.57 5.15 1.01e+00 9.80e-01 2.60e+01 angle pdb=" O3' A R 210 " pdb=" C3' A R 210 " pdb=" C2' A R 210 " ideal model delta sigma weight residual 113.70 121.17 -7.47 1.50e+00 4.44e-01 2.48e+01 ... (remaining 12039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.22: 4669 33.22 - 66.44: 471 66.44 - 99.66: 49 99.66 - 132.87: 2 132.87 - 166.09: 1 Dihedral angle restraints: 5192 sinusoidal: 3929 harmonic: 1263 Sorted by residual: dihedral pdb=" O4' A R 123 " pdb=" C1' A R 123 " pdb=" N9 A R 123 " pdb=" C4 A R 123 " ideal model delta sinusoidal sigma weight residual 68.00 151.57 -83.57 1 1.70e+01 3.46e-03 2.95e+01 dihedral pdb=" O4' U R 205 " pdb=" C1' U R 205 " pdb=" N1 U R 205 " pdb=" C2 U R 205 " ideal model delta sinusoidal sigma weight residual -160.00 -88.78 -71.22 1 1.50e+01 4.44e-03 2.89e+01 dihedral pdb=" CA THR A 282 " pdb=" C THR A 282 " pdb=" N LEU A 283 " pdb=" CA LEU A 283 " ideal model delta harmonic sigma weight residual -180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 5189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1355 0.090 - 0.181: 117 0.181 - 0.271: 10 0.271 - 0.362: 5 0.362 - 0.452: 3 Chirality restraints: 1490 Sorted by residual: chirality pdb=" P DG P 1 " pdb=" OP1 DG P 1 " pdb=" OP2 DG P 1 " pdb=" O5' DG P 1 " both_signs ideal model delta sigma weight residual True 2.35 2.80 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" P DT P 5 " pdb=" OP1 DT P 5 " pdb=" OP2 DT P 5 " pdb=" O5' DT P 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.73 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" P DA P 2 " pdb=" OP1 DA P 2 " pdb=" OP2 DA P 2 " pdb=" O5' DA P 2 " both_signs ideal model delta sigma weight residual True 2.35 -2.71 -0.37 2.00e-01 2.50e+01 3.34e+00 ... (remaining 1487 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G R 33 " -0.030 2.00e-02 2.50e+03 1.41e-02 5.97e+00 pdb=" N9 G R 33 " 0.035 2.00e-02 2.50e+03 pdb=" C8 G R 33 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G R 33 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G R 33 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G R 33 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G R 33 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G R 33 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G R 33 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G R 33 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G R 33 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G R 33 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 404 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C ASN A 404 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN A 404 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 405 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 383 " 0.186 9.50e-02 1.11e+02 8.38e-02 5.06e+00 pdb=" NE ARG A 383 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 383 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 383 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 383 " 0.002 2.00e-02 2.50e+03 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.70: 412 2.70 - 3.31: 6858 3.31 - 3.92: 17454 3.92 - 4.53: 22336 4.53 - 5.14: 29347 Nonbonded interactions: 76407 Sorted by model distance: nonbonded pdb=" OD2 ASP A 140 " pdb="MG MG A 501 " model vdw 2.090 2.170 nonbonded pdb=" O LYS A 55 " pdb=" OG SER A 64 " model vdw 2.334 3.040 nonbonded pdb=" OG1 THR A 208 " pdb=" OD2 ASP A 211 " model vdw 2.393 3.040 nonbonded pdb=" OG SER A 195 " pdb=" OP2 C R 218 " model vdw 2.404 3.040 nonbonded pdb=" NH2 ARG A 217 " pdb=" O6 G R 22 " model vdw 2.407 3.120 ... (remaining 76402 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.970 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 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 0.069 8235 Z= 0.344 Angle : 1.031 13.142 12044 Z= 0.563 Chirality : 0.057 0.452 1490 Planarity : 0.008 0.084 803 Dihedral : 21.515 166.093 4378 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.80 % Allowed : 8.31 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.37), residues: 423 helix: -0.44 (0.31), residues: 205 sheet: 1.13 (0.68), residues: 57 loop : -0.29 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 8 HIS 0.008 0.002 HIS A 263 PHE 0.021 0.004 PHE A 328 TYR 0.023 0.003 TYR A 83 ARG 0.015 0.002 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.539 Fit side-chains REVERT: A 390 ARG cc_start: 0.8246 (mtm180) cc_final: 0.8028 (mtp180) outliers start: 3 outliers final: 3 residues processed: 43 average time/residue: 1.5721 time to fit residues: 71.0752 Evaluate side-chains 35 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 294 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 10.0000 chunk 46 optimal weight: 30.0000 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.169421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.110338 restraints weight = 8279.301| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.23 r_work: 0.2757 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8235 Z= 0.153 Angle : 0.531 6.070 12044 Z= 0.279 Chirality : 0.035 0.219 1490 Planarity : 0.004 0.045 803 Dihedral : 22.038 178.165 3495 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.07 % Allowed : 9.38 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.40), residues: 423 helix: 1.17 (0.35), residues: 212 sheet: 1.27 (0.69), residues: 57 loop : 0.02 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 157 HIS 0.002 0.001 HIS A 263 PHE 0.011 0.001 PHE A 328 TYR 0.010 0.001 TYR A 245 ARG 0.003 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.595 Fit side-chains REVERT: A 159 LYS cc_start: 0.8708 (mttt) cc_final: 0.8504 (tttp) REVERT: A 250 ASP cc_start: 0.8539 (m-30) cc_final: 0.8265 (m-30) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 1.7334 time to fit residues: 74.5405 Evaluate side-chains 34 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 130 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 0.0070 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.170626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109934 restraints weight = 8472.065| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.50 r_work: 0.2750 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8235 Z= 0.124 Angle : 0.474 5.746 12044 Z= 0.249 Chirality : 0.032 0.218 1490 Planarity : 0.004 0.042 803 Dihedral : 21.888 177.742 3491 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.54 % Allowed : 10.99 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.41), residues: 423 helix: 1.77 (0.36), residues: 212 sheet: 1.56 (0.68), residues: 55 loop : 0.10 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 PHE 0.009 0.001 PHE A 44 TYR 0.009 0.001 TYR A 86 ARG 0.003 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.526 Fit side-chains REVERT: A 68 LYS cc_start: 0.7812 (tttm) cc_final: 0.7318 (mtpt) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 1.7801 time to fit residues: 68.8723 Evaluate side-chains 32 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.0570 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.170708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.108351 restraints weight = 8276.617| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.25 r_work: 0.2759 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8235 Z= 0.143 Angle : 0.475 5.001 12044 Z= 0.249 Chirality : 0.031 0.219 1490 Planarity : 0.004 0.041 803 Dihedral : 21.505 163.908 3491 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.61 % Allowed : 11.80 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.41), residues: 423 helix: 1.90 (0.37), residues: 212 sheet: 1.64 (0.69), residues: 55 loop : 0.06 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 157 HIS 0.003 0.001 HIS A 39 PHE 0.009 0.001 PHE A 328 TYR 0.010 0.001 TYR A 86 ARG 0.003 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.557 Fit side-chains REVERT: A 65 LYS cc_start: 0.6861 (pttm) cc_final: 0.6334 (pttp) REVERT: A 68 LYS cc_start: 0.7783 (tttm) cc_final: 0.7283 (mtpt) outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 1.6121 time to fit residues: 64.5261 Evaluate side-chains 36 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 58 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 0.0020 overall best weight: 2.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.168239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105968 restraints weight = 8239.388| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.28 r_work: 0.2711 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8235 Z= 0.252 Angle : 0.554 6.374 12044 Z= 0.288 Chirality : 0.035 0.223 1490 Planarity : 0.005 0.043 803 Dihedral : 21.475 160.067 3491 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.14 % Allowed : 11.80 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.41), residues: 423 helix: 1.69 (0.37), residues: 211 sheet: 1.40 (0.67), residues: 55 loop : -0.19 (0.48), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 157 HIS 0.003 0.001 HIS A 170 PHE 0.012 0.002 PHE A 328 TYR 0.012 0.002 TYR A 86 ARG 0.004 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.593 Fit side-chains REVERT: A 68 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7460 (tttm) outliers start: 8 outliers final: 3 residues processed: 39 average time/residue: 1.6345 time to fit residues: 67.1035 Evaluate side-chains 38 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 191 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 30.0000 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 31 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 30.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.170016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110011 restraints weight = 8217.271| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.11 r_work: 0.2742 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8235 Z= 0.140 Angle : 0.486 5.152 12044 Z= 0.256 Chirality : 0.032 0.222 1490 Planarity : 0.004 0.041 803 Dihedral : 21.412 161.029 3491 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.34 % Allowed : 12.60 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.41), residues: 423 helix: 1.92 (0.37), residues: 212 sheet: 1.39 (0.67), residues: 55 loop : 0.02 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 157 HIS 0.002 0.001 HIS A 77 PHE 0.009 0.001 PHE A 328 TYR 0.010 0.001 TYR A 14 ARG 0.003 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.556 Fit side-chains REVERT: A 68 LYS cc_start: 0.7763 (tttm) cc_final: 0.7224 (mtpt) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 1.5445 time to fit residues: 60.2243 Evaluate side-chains 37 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 191 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 30.0000 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.169704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110419 restraints weight = 8243.795| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.22 r_work: 0.2746 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8235 Z= 0.132 Angle : 0.468 5.095 12044 Z= 0.245 Chirality : 0.031 0.215 1490 Planarity : 0.004 0.042 803 Dihedral : 21.342 161.001 3491 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.34 % Allowed : 12.87 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.42), residues: 423 helix: 2.03 (0.37), residues: 212 sheet: 1.51 (0.68), residues: 55 loop : 0.06 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 157 HIS 0.002 0.001 HIS A 263 PHE 0.008 0.001 PHE A 328 TYR 0.011 0.001 TYR A 86 ARG 0.003 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.594 Fit side-chains REVERT: A 68 LYS cc_start: 0.7764 (tttm) cc_final: 0.7209 (mtpt) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 1.6631 time to fit residues: 69.8726 Evaluate side-chains 40 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 191 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.168436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.107583 restraints weight = 8277.070| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.22 r_work: 0.2723 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8235 Z= 0.196 Angle : 0.498 5.189 12044 Z= 0.260 Chirality : 0.033 0.220 1490 Planarity : 0.004 0.045 803 Dihedral : 21.345 161.090 3491 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.34 % Allowed : 13.14 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.41), residues: 423 helix: 1.94 (0.37), residues: 211 sheet: 1.43 (0.67), residues: 55 loop : -0.07 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 PHE 0.011 0.001 PHE A 328 TYR 0.012 0.002 TYR A 245 ARG 0.003 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.525 Fit side-chains REVERT: A 68 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7239 (mtpt) outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 1.6426 time to fit residues: 67.3345 Evaluate side-chains 41 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 191 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 56 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.168460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107094 restraints weight = 8320.592| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.24 r_work: 0.2709 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8235 Z= 0.199 Angle : 0.497 5.213 12044 Z= 0.260 Chirality : 0.033 0.220 1490 Planarity : 0.004 0.045 803 Dihedral : 21.343 161.211 3491 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.34 % Allowed : 13.40 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.41), residues: 423 helix: 1.93 (0.37), residues: 211 sheet: 1.41 (0.67), residues: 55 loop : -0.08 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 PHE 0.010 0.001 PHE A 328 TYR 0.012 0.002 TYR A 245 ARG 0.003 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.604 Fit side-chains REVERT: A 68 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7192 (mtpt) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 1.6553 time to fit residues: 66.2279 Evaluate side-chains 40 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 191 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 43 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.166269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.104420 restraints weight = 8270.235| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.41 r_work: 0.2658 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8235 Z= 0.322 Angle : 0.603 6.215 12044 Z= 0.312 Chirality : 0.038 0.224 1490 Planarity : 0.005 0.048 803 Dihedral : 21.530 163.213 3491 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.61 % Allowed : 13.14 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.40), residues: 423 helix: 1.62 (0.36), residues: 211 sheet: 1.51 (0.65), residues: 53 loop : -0.19 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 157 HIS 0.003 0.001 HIS A 263 PHE 0.014 0.002 PHE A 328 TYR 0.014 0.002 TYR A 245 ARG 0.003 0.001 ARG A 266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.559 Fit side-chains REVERT: A 66 THR cc_start: 0.7629 (m) cc_final: 0.6834 (p) REVERT: A 68 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7447 (tttm) outliers start: 6 outliers final: 3 residues processed: 41 average time/residue: 1.5437 time to fit residues: 66.8164 Evaluate side-chains 40 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 191 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 51.8084 > 50: distance: 65 - 85: 3.207 distance: 70 - 96: 3.660 distance: 75 - 105: 3.404 distance: 82 - 113: 7.418 distance: 86 - 89: 3.260 distance: 90 - 91: 3.062 distance: 92 - 93: 3.102 distance: 98 - 99: 5.303 distance: 100 - 101: 4.342 distance: 101 - 102: 3.308 distance: 102 - 103: 4.772 distance: 106 - 109: 3.004 distance: 107 - 108: 4.061 distance: 107 - 113: 3.568 distance: 113 - 114: 6.490 distance: 114 - 115: 13.223 distance: 114 - 117: 5.206 distance: 115 - 116: 28.447 distance: 115 - 122: 22.157 distance: 117 - 118: 8.182 distance: 118 - 119: 12.423 distance: 119 - 120: 10.467 distance: 120 - 121: 13.198 distance: 122 - 123: 4.854 distance: 122 - 128: 13.391 distance: 123 - 124: 10.431 distance: 123 - 126: 10.926 distance: 124 - 125: 5.106 distance: 124 - 129: 3.304 distance: 125 - 155: 9.552 distance: 126 - 127: 11.883 distance: 127 - 128: 5.548 distance: 130 - 131: 3.778 distance: 130 - 133: 9.931 distance: 131 - 132: 4.596 distance: 131 - 137: 4.700 distance: 132 - 166: 7.788 distance: 133 - 134: 7.363 distance: 134 - 135: 6.296 distance: 134 - 136: 12.406 distance: 137 - 138: 3.689 distance: 138 - 139: 5.587 distance: 139 - 140: 3.433 distance: 139 - 146: 4.030 distance: 140 - 174: 6.391 distance: 141 - 142: 4.396 distance: 142 - 143: 6.640 distance: 143 - 144: 3.118 distance: 143 - 145: 9.221 distance: 146 - 147: 7.032 distance: 147 - 150: 7.052 distance: 148 - 149: 6.535 distance: 148 - 155: 3.481 distance: 149 - 183: 8.776 distance: 150 - 151: 5.505 distance: 151 - 152: 11.772 distance: 152 - 153: 5.305 distance: 153 - 154: 8.391 distance: 155 - 156: 3.907 distance: 156 - 157: 3.182 distance: 157 - 158: 4.140 distance: 158 - 191: 6.066 distance: 159 - 160: 8.391 distance: 160 - 161: 3.936 distance: 161 - 162: 3.834 distance: 162 - 163: 5.036 distance: 163 - 164: 6.408 distance: 163 - 165: 4.827 distance: 167 - 168: 3.325 distance: 171 - 172: 4.919 distance: 171 - 173: 4.849