Starting phenix.real_space_refine on Wed Mar 5 17:40:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7u_39828/03_2025/8z7u_39828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7u_39828/03_2025/8z7u_39828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7u_39828/03_2025/8z7u_39828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7u_39828/03_2025/8z7u_39828.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7u_39828/03_2025/8z7u_39828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7u_39828/03_2025/8z7u_39828.cif" } resolution = 3.1 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= 0.002 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2118 2.51 5 N 469 2.21 5 O 532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3135 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3098 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'2TA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.77, per 1000 atoms: 0.88 Number of scatterers: 3135 At special positions: 0 Unit cell: (63, 68, 69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 532 8.00 N 469 7.00 C 2118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 335.4 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 86.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.636A pdb=" N THR A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.742A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 79 through 100 removed outlier: 3.685A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 131 removed outlier: 4.318A pdb=" N THR A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 165 removed outlier: 3.787A pdb=" N SER A 163 " --> pdb=" O GLN A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 189 Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 278 through 307 removed outlier: 4.173A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 337 removed outlier: 3.549A pdb=" N TYR A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 366 Processing helix chain 'A' and resid 368 through 399 removed outlier: 4.603A pdb=" N ASN A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 426 removed outlier: 3.585A pdb=" N VAL A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 461 removed outlier: 3.809A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 451 1.28 - 1.42: 947 1.42 - 1.55: 1801 1.55 - 1.68: 4 1.68 - 1.82: 28 Bond restraints: 3231 Sorted by residual: bond pdb=" CAO 2TA A 501 " pdb=" NAP 2TA A 501 " ideal model delta sigma weight residual 1.444 1.171 0.273 2.00e-02 2.50e+03 1.86e+02 bond pdb=" CAS 2TA A 501 " pdb=" CAT 2TA A 501 " ideal model delta sigma weight residual 1.532 1.323 0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" CAQ 2TA A 501 " pdb=" NAP 2TA A 501 " ideal model delta sigma weight residual 1.454 1.258 0.196 2.00e-02 2.50e+03 9.64e+01 bond pdb=" C2 2TA A 501 " pdb=" N1 2TA A 501 " ideal model delta sigma weight residual 1.322 1.489 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" CAY 2TA A 501 " pdb=" CAZ 2TA A 501 " ideal model delta sigma weight residual 1.386 1.534 -0.148 2.00e-02 2.50e+03 5.50e+01 ... (remaining 3226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 4363 3.39 - 6.78: 47 6.78 - 10.17: 6 10.17 - 13.55: 2 13.55 - 16.94: 1 Bond angle restraints: 4419 Sorted by residual: angle pdb=" OBJ 2TA A 501 " pdb=" SBD 2TA A 501 " pdb=" OBK 2TA A 501 " ideal model delta sigma weight residual 118.13 101.19 16.94 3.00e+00 1.11e-01 3.19e+01 angle pdb=" C VAL A 72 " pdb=" N LEU A 73 " pdb=" CA LEU A 73 " ideal model delta sigma weight residual 122.49 130.59 -8.10 1.55e+00 4.16e-01 2.73e+01 angle pdb=" CA LEU A 67 " pdb=" C LEU A 67 " pdb=" O LEU A 67 " ideal model delta sigma weight residual 120.42 114.95 5.47 1.06e+00 8.90e-01 2.66e+01 angle pdb=" C PHE A 71 " pdb=" N VAL A 72 " pdb=" CA VAL A 72 " ideal model delta sigma weight residual 121.34 113.68 7.66 1.62e+00 3.81e-01 2.24e+01 angle pdb=" CA PHE A 71 " pdb=" CB PHE A 71 " pdb=" CG PHE A 71 " ideal model delta sigma weight residual 113.80 118.17 -4.37 1.00e+00 1.00e+00 1.91e+01 ... (remaining 4414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.60: 1743 33.60 - 67.20: 72 67.20 - 100.80: 7 100.80 - 134.41: 0 134.41 - 168.01: 2 Dihedral angle restraints: 1824 sinusoidal: 675 harmonic: 1149 Sorted by residual: dihedral pdb=" CAG 2TA A 501 " pdb=" C2 2TA A 501 " pdb=" NAF 2TA A 501 " pdb=" N1 2TA A 501 " ideal model delta sinusoidal sigma weight residual -0.72 -168.73 168.01 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" NAP 2TA A 501 " pdb=" CAN 2TA A 501 " pdb=" CAO 2TA A 501 " pdb=" OAM 2TA A 501 " ideal model delta sinusoidal sigma weight residual -75.66 64.46 -140.12 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" C PHE A 71 " pdb=" N PHE A 71 " pdb=" CA PHE A 71 " pdb=" CB PHE A 71 " ideal model delta harmonic sigma weight residual -122.60 -132.92 10.32 0 2.50e+00 1.60e-01 1.70e+01 ... (remaining 1821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 431 0.062 - 0.124: 67 0.124 - 0.185: 6 0.185 - 0.247: 0 0.247 - 0.309: 1 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA PHE A 71 " pdb=" N PHE A 71 " pdb=" C PHE A 71 " pdb=" CB PHE A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ASN A 399 " pdb=" N ASN A 399 " pdb=" C ASN A 399 " pdb=" CB ASN A 399 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CA VAL A 70 " pdb=" N VAL A 70 " pdb=" C VAL A 70 " pdb=" CB VAL A 70 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 502 not shown) Planarity restraints: 526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 66 " -0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C LEU A 66 " 0.072 2.00e-02 2.50e+03 pdb=" O LEU A 66 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU A 67 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 72 " 0.011 2.00e-02 2.50e+03 2.37e-02 5.64e+00 pdb=" C VAL A 72 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL A 72 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 73 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 144 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ARG A 144 " -0.038 2.00e-02 2.50e+03 pdb=" O ARG A 144 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 145 " 0.013 2.00e-02 2.50e+03 ... (remaining 523 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 532 2.75 - 3.29: 3336 3.29 - 3.83: 5582 3.83 - 4.36: 6599 4.36 - 4.90: 11253 Nonbonded interactions: 27302 Sorted by model distance: nonbonded pdb=" OE1 GLU A 110 " pdb=" NAF 2TA A 501 " model vdw 2.218 3.120 nonbonded pdb=" OH TYR A 128 " pdb=" OG SER A 140 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 38 " pdb=" O LEU A 97 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASP A 75 " pdb=" OH TYR A 79 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR A 126 " pdb=" O PRO A 191 " model vdw 2.309 3.040 ... (remaining 27297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.650 Find NCS groups from input model: 0.030 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.014 0.273 3231 Z= 0.850 Angle : 0.902 16.943 4419 Z= 0.490 Chirality : 0.045 0.309 505 Planarity : 0.006 0.042 526 Dihedral : 19.012 168.006 1090 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.90 % Allowed : 24.62 % Favored : 74.47 % Cbeta Deviations : 0.27 % 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: -0.32 (0.43), residues: 383 helix: 0.01 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -0.63 (0.91), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.021 0.001 PHE A 71 TYR 0.025 0.001 TYR A 280 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.300 Fit side-chains REVERT: A 71 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8665 (p90) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.1646 time to fit residues: 8.2095 Evaluate side-chains 38 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.134063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.110922 restraints weight = 3547.536| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.76 r_work: 0.3198 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3231 Z= 0.266 Angle : 0.671 9.964 4419 Z= 0.335 Chirality : 0.044 0.172 505 Planarity : 0.004 0.028 526 Dihedral : 13.784 177.859 443 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.70 % Allowed : 23.42 % Favored : 73.87 % 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: 0.89 (0.43), residues: 383 helix: 0.80 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -0.07 (0.93), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.025 0.002 PHE A 71 TYR 0.018 0.002 TYR A 280 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.299 Fit side-chains REVERT: A 401 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5301 (tp30) outliers start: 9 outliers final: 3 residues processed: 51 average time/residue: 0.1216 time to fit residues: 8.0457 Evaluate side-chains 40 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.150490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129561 restraints weight = 3344.479| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.58 r_work: 0.3301 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3231 Z= 0.237 Angle : 0.616 9.409 4419 Z= 0.308 Chirality : 0.042 0.171 505 Planarity : 0.004 0.029 526 Dihedral : 12.322 174.909 439 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.30 % Allowed : 23.42 % Favored : 73.27 % 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: 1.52 (0.43), residues: 383 helix: 1.18 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 0.58 (0.90), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.024 0.001 PHE A 71 TYR 0.020 0.002 TYR A 280 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.297 Fit side-chains REVERT: A 401 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.5474 (tp30) outliers start: 11 outliers final: 4 residues processed: 53 average time/residue: 0.1194 time to fit residues: 8.2580 Evaluate side-chains 45 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.0870 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3708 r_free = 0.3708 target = 0.150039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.129146 restraints weight = 3383.670| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.60 r_work: 0.3269 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3231 Z= 0.242 Angle : 0.605 9.201 4419 Z= 0.305 Chirality : 0.042 0.168 505 Planarity : 0.004 0.032 526 Dihedral : 11.223 167.905 439 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.30 % Allowed : 23.72 % Favored : 72.97 % 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: 1.65 (0.43), residues: 383 helix: 1.31 (0.28), residues: 316 sheet: None (None), residues: 0 loop : 0.44 (0.87), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.024 0.001 PHE A 71 TYR 0.021 0.002 TYR A 280 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.329 Fit side-chains REVERT: A 280 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: A 401 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5490 (tp30) outliers start: 11 outliers final: 3 residues processed: 53 average time/residue: 0.1185 time to fit residues: 8.2216 Evaluate side-chains 47 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3707 r_free = 0.3707 target = 0.150060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129134 restraints weight = 3384.375| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.59 r_work: 0.3310 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3231 Z= 0.244 Angle : 0.604 11.040 4419 Z= 0.301 Chirality : 0.041 0.172 505 Planarity : 0.004 0.034 526 Dihedral : 10.096 162.594 439 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.60 % Allowed : 22.82 % Favored : 73.57 % 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: 1.77 (0.43), residues: 383 helix: 1.41 (0.28), residues: 316 sheet: None (None), residues: 0 loop : 0.39 (0.87), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.023 0.001 PHE A 71 TYR 0.022 0.002 TYR A 280 ARG 0.001 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.299 Fit side-chains REVERT: A 401 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5486 (tp30) outliers start: 12 outliers final: 6 residues processed: 57 average time/residue: 0.1127 time to fit residues: 8.5283 Evaluate side-chains 49 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3595 r_free = 0.3595 target = 0.142782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.120643 restraints weight = 3518.578| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.70 r_work: 0.3199 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3231 Z= 0.224 Angle : 0.594 10.987 4419 Z= 0.296 Chirality : 0.042 0.166 505 Planarity : 0.004 0.035 526 Dihedral : 9.656 158.574 439 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.90 % Allowed : 21.62 % Favored : 74.47 % 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: 1.85 (0.43), residues: 383 helix: 1.42 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 0.60 (0.90), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.023 0.001 PHE A 71 TYR 0.020 0.001 TYR A 280 ARG 0.001 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.294 Fit side-chains REVERT: A 401 GLU cc_start: 0.5971 (OUTLIER) cc_final: 0.5427 (tp30) outliers start: 13 outliers final: 6 residues processed: 60 average time/residue: 0.1149 time to fit residues: 9.1567 Evaluate side-chains 51 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3644 r_free = 0.3644 target = 0.144734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124306 restraints weight = 3461.758| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.53 r_work: 0.3366 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3231 Z= 0.238 Angle : 0.609 10.970 4419 Z= 0.302 Chirality : 0.042 0.163 505 Planarity : 0.004 0.035 526 Dihedral : 9.517 158.190 439 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.30 % Allowed : 22.52 % Favored : 74.17 % 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: 1.89 (0.43), residues: 383 helix: 1.46 (0.28), residues: 319 sheet: None (None), residues: 0 loop : 0.54 (0.89), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.024 0.001 PHE A 71 TYR 0.020 0.001 TYR A 280 ARG 0.001 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.304 Fit side-chains REVERT: A 401 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5562 (tp30) outliers start: 11 outliers final: 5 residues processed: 55 average time/residue: 0.1086 time to fit residues: 7.8707 Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3599 r_free = 0.3599 target = 0.142432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120041 restraints weight = 3403.116| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.73 r_work: 0.3273 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3231 Z= 0.263 Angle : 0.612 11.439 4419 Z= 0.305 Chirality : 0.043 0.167 505 Planarity : 0.004 0.036 526 Dihedral : 9.279 155.542 439 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.30 % Allowed : 23.12 % Favored : 73.57 % 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: 1.95 (0.43), residues: 383 helix: 1.53 (0.28), residues: 316 sheet: None (None), residues: 0 loop : 0.44 (0.87), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.024 0.001 PHE A 71 TYR 0.020 0.002 TYR A 280 ARG 0.001 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.324 Fit side-chains REVERT: A 365 TYR cc_start: 0.8337 (m-80) cc_final: 0.8050 (m-80) REVERT: A 401 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5386 (tp30) outliers start: 11 outliers final: 8 residues processed: 52 average time/residue: 0.1139 time to fit residues: 7.8029 Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 422 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 4.9990 chunk 6 optimal weight: 0.0050 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.0020 chunk 8 optimal weight: 0.9990 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3698 r_free = 0.3698 target = 0.149574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127788 restraints weight = 3424.293| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.68 r_work: 0.3168 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3231 Z= 0.228 Angle : 0.594 11.116 4419 Z= 0.296 Chirality : 0.042 0.180 505 Planarity : 0.004 0.036 526 Dihedral : 9.143 154.463 439 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.00 % Allowed : 23.12 % Favored : 73.87 % 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: 2.00 (0.43), residues: 383 helix: 1.53 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.59 (0.91), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.023 0.001 PHE A 71 TYR 0.020 0.001 TYR A 280 ARG 0.001 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.299 Fit side-chains REVERT: A 151 TYR cc_start: 0.8308 (t80) cc_final: 0.8068 (t80) REVERT: A 365 TYR cc_start: 0.8318 (m-80) cc_final: 0.8043 (m-80) REVERT: A 401 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5337 (tp30) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 0.1144 time to fit residues: 7.8439 Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 54.526 > 50: distance: 3 - 23: 3.486 distance: 8 - 29: 4.512 distance: 13 - 37: 8.779 distance: 18 - 48: 10.580 distance: 23 - 24: 5.471 distance: 24 - 25: 3.284 distance: 24 - 27: 10.664 distance: 25 - 26: 11.143 distance: 25 - 29: 4.368 distance: 26 - 52: 25.357 distance: 27 - 28: 5.549 distance: 29 - 30: 8.942 distance: 30 - 31: 15.264 distance: 30 - 33: 5.816 distance: 31 - 32: 17.546 distance: 31 - 37: 12.694 distance: 32 - 63: 23.894 distance: 33 - 34: 6.460 distance: 34 - 35: 10.796 distance: 34 - 36: 18.190 distance: 37 - 38: 3.286 distance: 38 - 39: 7.477 distance: 38 - 41: 5.426 distance: 39 - 40: 11.200 distance: 39 - 48: 8.219 distance: 40 - 74: 13.761 distance: 42 - 43: 4.301 distance: 42 - 44: 5.519 distance: 43 - 45: 15.299 distance: 44 - 46: 10.444 distance: 45 - 47: 4.115 distance: 46 - 47: 7.525 distance: 48 - 49: 12.940 distance: 49 - 50: 14.009 distance: 50 - 51: 12.855 distance: 50 - 52: 17.011 distance: 52 - 53: 13.995 distance: 53 - 54: 8.016 distance: 53 - 56: 14.835 distance: 54 - 55: 18.517 distance: 54 - 63: 22.107 distance: 56 - 57: 17.405 distance: 57 - 58: 15.267 distance: 57 - 59: 8.301 distance: 58 - 60: 17.287 distance: 59 - 61: 20.598 distance: 60 - 62: 7.975 distance: 61 - 62: 23.151 distance: 63 - 64: 10.457 distance: 64 - 65: 17.620 distance: 64 - 67: 10.752 distance: 65 - 66: 20.705 distance: 65 - 74: 11.859 distance: 67 - 68: 11.423 distance: 68 - 69: 9.342 distance: 68 - 70: 7.245 distance: 69 - 71: 19.054 distance: 70 - 72: 17.049 distance: 71 - 73: 12.701 distance: 72 - 73: 19.378 distance: 74 - 75: 7.284 distance: 75 - 76: 7.506 distance: 75 - 78: 6.992 distance: 76 - 77: 10.774 distance: 76 - 80: 7.666 distance: 78 - 79: 7.648 distance: 80 - 81: 8.097 distance: 81 - 82: 6.403 distance: 81 - 84: 12.830 distance: 82 - 83: 3.577 distance: 82 - 88: 6.957 distance: 84 - 85: 25.022 distance: 85 - 86: 30.599 distance: 86 - 87: 29.721 distance: 88 - 89: 7.238 distance: 89 - 90: 7.710 distance: 89 - 92: 7.989 distance: 90 - 91: 7.449 distance: 90 - 96: 10.784 distance: 93 - 94: 17.975 distance: 94 - 95: 25.803 distance: 96 - 97: 8.492 distance: 97 - 98: 11.125 distance: 97 - 100: 12.192 distance: 98 - 107: 12.132 distance: 100 - 101: 10.326 distance: 101 - 102: 10.401 distance: 102 - 103: 9.535 distance: 103 - 104: 10.153 distance: 104 - 105: 10.987 distance: 104 - 106: 17.226