Starting phenix.real_space_refine on Mon Feb 10 22:40:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7u_39828/02_2025/8z7u_39828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7u_39828/02_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_39828/02_2025/8z7u_39828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7u_39828/02_2025/8z7u_39828.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7u_39828/02_2025/8z7u_39828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7u_39828/02_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-5592/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: 2.57, per 1000 atoms: 0.82 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: 0.82 Conformation dependent library (CDL) restraints added in 343.8 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: 0.27 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: 0.86 Time building geometry restraints manager: 0.96 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: 0.720 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.290 ------------------------------------------------------------------------------- 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 : 0.344 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: 0.1648 time to fit residues: 8.1969 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 : 0.252 ------------------------------------------------------------------------------- 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: 0.9990 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 = 0.110921 restraints weight = 3547.536| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.76 r_work: 0.3200 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.318 Fit side-chains REVERT: A 401 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5304 (tp30) outliers start: 9 outliers final: 3 residues processed: 51 average time/residue: 0.1252 time to fit residues: 8.2330 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 : 0.316 ------------------------------------------------------------------------------- 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: 0.5980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.0040 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.150648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129716 restraints weight = 3344.453| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.58 r_work: 0.3302 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3231 Z= 0.231 Angle : 0.613 9.363 4419 Z= 0.306 Chirality : 0.042 0.171 505 Planarity : 0.004 0.030 526 Dihedral : 12.344 175.124 439 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 1.52 (0.43), residues: 383 helix: 1.18 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 0.57 (0.90), 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 0.002 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 : 0.332 Fit side-chains REVERT: A 401 GLU cc_start: 0.5931 (OUTLIER) cc_final: 0.5465 (tp30) outliers start: 11 outliers final: 4 residues processed: 53 average time/residue: 0.1186 time to fit residues: 8.3248 Evaluate side-chains 44 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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: 0.8980 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 18 optimal weight: 0.3980 chunk 2 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.151150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.130331 restraints weight = 3377.747| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.59 r_work: 0.3257 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3231 Z= 0.215 Angle : 0.595 8.857 4419 Z= 0.299 Chirality : 0.041 0.163 505 Planarity : 0.004 0.033 526 Dihedral : 11.315 169.186 439 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.00 % Allowed : 23.72 % 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: 1.72 (0.43), residues: 383 helix: 1.32 (0.28), residues: 319 sheet: None (None), residues: 0 loop : 0.65 (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 0.021 0.001 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 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.346 Fit side-chains REVERT: A 280 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.6135 (m-80) REVERT: A 401 GLU cc_start: 0.5881 (OUTLIER) cc_final: 0.5478 (tp30) outliers start: 10 outliers final: 3 residues processed: 52 average time/residue: 0.1203 time to fit residues: 8.1705 Evaluate side-chains 46 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.149143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128136 restraints weight = 3390.698| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.60 r_work: 0.3255 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3231 Z= 0.277 Angle : 0.618 11.349 4419 Z= 0.308 Chirality : 0.042 0.178 505 Planarity : 0.004 0.035 526 Dihedral : 10.223 163.212 439 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.30 % Allowed : 22.82 % 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: 1.81 (0.43), residues: 383 helix: 1.41 (0.28), residues: 315 sheet: None (None), residues: 0 loop : 0.55 (0.87), residues: 68 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 0.022 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 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: 0.5984 (OUTLIER) cc_final: 0.5466 (tp30) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.1141 time to fit residues: 8.3808 Evaluate side-chains 49 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.0040 chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.150783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129802 restraints weight = 3449.462| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.60 r_work: 0.3296 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3231 Z= 0.221 Angle : 0.593 10.872 4419 Z= 0.295 Chirality : 0.042 0.169 505 Planarity : 0.004 0.035 526 Dihedral : 9.684 158.775 439 Min Nonbonded Distance : 2.599 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 : 0.62 (0.91), 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 : 0.350 Fit side-chains REVERT: A 151 TYR cc_start: 0.8367 (t80) cc_final: 0.8154 (t80) REVERT: A 401 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5468 (tp30) outliers start: 13 outliers final: 6 residues processed: 60 average time/residue: 0.1124 time to fit residues: 8.8778 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 : 0.353 ------------------------------------------------------------------------------- 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: 2.9990 chunk 9 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.145863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124964 restraints weight = 3389.296| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.57 r_work: 0.3277 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3231 Z= 0.252 Angle : 0.616 11.278 4419 Z= 0.305 Chirality : 0.042 0.174 505 Planarity : 0.004 0.036 526 Dihedral : 9.563 158.234 439 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.00 % Allowed : 22.82 % 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: 1.85 (0.43), residues: 383 helix: 1.46 (0.29), residues: 317 sheet: None (None), residues: 0 loop : 0.43 (0.89), residues: 66 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 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.329 Fit side-chains REVERT: A 151 TYR cc_start: 0.8286 (t80) cc_final: 0.8074 (t80) REVERT: A 401 GLU cc_start: 0.5971 (OUTLIER) cc_final: 0.5420 (tp30) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 0.1103 time to fit residues: 7.8540 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 : 0.307 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.134678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.111409 restraints weight = 3497.029| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.78 r_work: 0.3294 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3231 Z= 0.228 Angle : 0.597 10.979 4419 Z= 0.297 Chirality : 0.042 0.178 505 Planarity : 0.004 0.036 526 Dihedral : 9.301 155.824 439 Min Nonbonded Distance : 2.512 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: 1.97 (0.43), residues: 383 helix: 1.51 (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 0.017 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 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 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.315 Fit side-chains REVERT: A 151 TYR cc_start: 0.8250 (t80) cc_final: 0.8012 (t80) REVERT: A 365 TYR cc_start: 0.8342 (m-80) cc_final: 0.8054 (m-80) REVERT: A 401 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5291 (tp30) outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 0.1146 time to fit residues: 8.3969 Evaluate side-chains 52 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 280 TYR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 5.9990 chunk 6 optimal weight: 0.0070 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.148007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126926 restraints weight = 3444.143| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.58 r_work: 0.3323 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2172 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= 0.225 Angle : 0.595 11.101 4419 Z= 0.297 Chirality : 0.042 0.173 505 Planarity : 0.004 0.036 526 Dihedral : 9.137 154.234 439 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.70 % Allowed : 22.82 % 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: 2.04 (0.44), residues: 383 helix: 1.51 (0.29), residues: 323 sheet: None (None), residues: 0 loop : 0.89 (0.96), residues: 60 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 0.023 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 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.340 Fit side-chains REVERT: A 151 TYR cc_start: 0.8326 (t80) cc_final: 0.8067 (t80) REVERT: A 365 TYR cc_start: 0.8325 (m-80) cc_final: 0.8076 (m-80) outliers start: 9 outliers final: 9 residues processed: 55 average time/residue: 0.1172 time to fit residues: 8.4503 Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 280 TYR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 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 = 0.3569 r_free = 0.3569 target = 0.140298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117930 restraints weight = 3418.574| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.73 r_work: 0.3285 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3231 Z= 0.261 Angle : 0.612 11.522 4419 Z= 0.304 Chirality : 0.043 0.179 505 Planarity : 0.004 0.036 526 Dihedral : 9.150 154.239 439 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: 2.02 (0.43), residues: 383 helix: 1.57 (0.28), residues: 317 sheet: None (None), residues: 0 loop : 0.51 (0.89), residues: 66 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 0.024 0.001 PHE A 71 TYR 0.020 0.001 TYR A 280 ARG 0.001 0.000 ARG A 402 ********************** REFINEMENT MACRO_CYCLE 10 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: 10 poor density : 47 time to evaluate : 0.321 Fit side-chains REVERT: A 151 TYR cc_start: 0.8330 (t80) cc_final: 0.8100 (t80) REVERT: A 365 TYR cc_start: 0.8340 (m-80) cc_final: 0.8081 (m-80) REVERT: A 401 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5374 (tp30) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.1076 time to fit residues: 7.7691 Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 280 TYR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.149595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.129107 restraints weight = 3373.608| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.54 r_work: 0.3150 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3231 Z= 0.269 Angle : 0.617 11.664 4419 Z= 0.307 Chirality : 0.043 0.168 505 Planarity : 0.004 0.036 526 Dihedral : 9.190 155.029 439 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.00 % Allowed : 23.42 % 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: 1.52 (0.28), residues: 317 sheet: None (None), residues: 0 loop : 0.50 (0.89), residues: 66 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 0.001 PHE A 71 TYR 0.020 0.001 TYR A 280 ARG 0.001 0.000 ARG A 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1830.26 seconds wall clock time: 33 minutes 18.93 seconds (1998.93 seconds total)