Starting phenix.real_space_refine on Fri Aug 22 13:17:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7u_39828/08_2025/8z7u_39828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7u_39828/08_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_39828/08_2025/8z7u_39828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7u_39828/08_2025/8z7u_39828.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7u_39828/08_2025/8z7u_39828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7u_39828/08_2025/8z7u_39828.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.11, per 1000 atoms: 0.35 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: 0.19 Conformation dependent library (CDL) restraints added in 86.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.07 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: 0.32 Time building geometry restraints manager: 0.26 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.010 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.750 ------------------------------------------------------------------------------- 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= 0.707 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 : 15.56 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 277 TYR 0.025 0.001 TYR A 280 PHE 0.021 0.001 PHE A 71 TRP 0.013 0.001 TRP A 94 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.01375 ( 3231) covalent geometry : angle 0.90212 ( 4419) hydrogen bonds : bond 0.19040 ( 245) hydrogen bonds : angle 7.97629 ( 735) *********************** 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 : 0.121 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: 0.0721 time to fit residues: 3.6900 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 : 0.115 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.133317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110068 restraints weight = 3546.743| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.77 r_work: 0.3186 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3231 Z= 0.183 Angle : 0.679 9.580 4419 Z= 0.339 Chirality : 0.044 0.168 505 Planarity : 0.004 0.029 526 Dihedral : 13.827 178.384 443 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.43), residues: 383 helix: 0.76 (0.28), residues: 327 sheet: None (None), residues: 0 loop : -0.06 (0.93), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.018 0.002 TYR A 280 PHE 0.027 0.002 PHE A 71 TRP 0.018 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 3231) covalent geometry : angle 0.67946 ( 4419) hydrogen bonds : bond 0.05315 ( 245) hydrogen bonds : angle 5.02293 ( 735) *********************** 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 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.114 Fit side-chains REVERT: A 401 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5259 (tp30) outliers start: 10 outliers final: 3 residues processed: 51 average time/residue: 0.0552 time to fit residues: 3.6647 Evaluate side-chains 42 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.144331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122355 restraints weight = 3405.982| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.70 r_work: 0.3256 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1554 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= 0.168 Angle : 0.624 9.683 4419 Z= 0.313 Chirality : 0.043 0.171 505 Planarity : 0.004 0.030 526 Dihedral : 12.261 173.418 439 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.43), residues: 383 helix: 1.19 (0.29), residues: 315 sheet: None (None), residues: 0 loop : 0.47 (0.87), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 138 TYR 0.020 0.002 TYR A 280 PHE 0.024 0.002 PHE A 71 TRP 0.019 0.002 TRP A 94 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3231) covalent geometry : angle 0.62449 ( 4419) hydrogen bonds : bond 0.04874 ( 245) hydrogen bonds : angle 4.66148 ( 735) *********************** 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 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.109 Fit side-chains REVERT: A 401 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5470 (tp30) outliers start: 12 outliers final: 5 residues processed: 56 average time/residue: 0.0490 time to fit residues: 3.6297 Evaluate side-chains 47 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.096 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.145139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.123239 restraints weight = 3413.602| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.71 r_work: 0.3224 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1770 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= 0.156 Angle : 0.609 9.292 4419 Z= 0.306 Chirality : 0.042 0.167 505 Planarity : 0.004 0.034 526 Dihedral : 11.297 167.983 439 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.43), residues: 383 helix: 1.27 (0.28), residues: 316 sheet: None (None), residues: 0 loop : 0.36 (0.87), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.021 0.002 TYR A 280 PHE 0.024 0.001 PHE A 71 TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3231) covalent geometry : angle 0.60900 ( 4419) hydrogen bonds : bond 0.04636 ( 245) hydrogen bonds : angle 4.53354 ( 735) *********************** 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: 10 poor density : 45 time to evaluate : 0.109 Fit side-chains REVERT: A 401 GLU cc_start: 0.5911 (OUTLIER) cc_final: 0.5434 (tp30) outliers start: 10 outliers final: 4 residues processed: 53 average time/residue: 0.0436 time to fit residues: 3.0692 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 : 0.120 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.0010 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.146059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.124349 restraints weight = 3406.556| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.69 r_work: 0.3237 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1875 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= 0.172 Angle : 0.615 11.220 4419 Z= 0.308 Chirality : 0.042 0.172 505 Planarity : 0.004 0.035 526 Dihedral : 10.311 162.965 439 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.20 % Allowed : 20.72 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.43), residues: 383 helix: 1.31 (0.28), residues: 315 sheet: None (None), residues: 0 loop : 0.46 (0.86), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 402 TYR 0.022 0.002 TYR A 280 PHE 0.024 0.001 PHE A 71 TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 3231) covalent geometry : angle 0.61542 ( 4419) hydrogen bonds : bond 0.04671 ( 245) hydrogen bonds : angle 4.51518 ( 735) *********************** 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 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.065 Fit side-chains REVERT: A 401 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.5446 (tp30) outliers start: 14 outliers final: 8 residues processed: 58 average time/residue: 0.0333 time to fit residues: 2.6004 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 : 0.079 ------------------------------------------------------------------------------- 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 129 SER 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 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 23 optimal weight: 0.0570 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 18 optimal weight: 0.0980 chunk 14 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.2498 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.153227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132630 restraints weight = 3375.104| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.58 r_work: 0.3316 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2046 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= 0.126 Angle : 0.580 10.392 4419 Z= 0.289 Chirality : 0.041 0.161 505 Planarity : 0.004 0.036 526 Dihedral : 9.640 158.143 439 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.20 % Allowed : 20.72 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.44), residues: 383 helix: 1.40 (0.29), residues: 322 sheet: None (None), residues: 0 loop : 0.78 (0.94), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 402 TYR 0.022 0.001 TYR A 280 PHE 0.022 0.001 PHE A 71 TRP 0.018 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3231) covalent geometry : angle 0.58026 ( 4419) hydrogen bonds : bond 0.04276 ( 245) hydrogen bonds : angle 4.31513 ( 735) *********************** 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 62 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 151 TYR cc_start: 0.8335 (t80) cc_final: 0.8124 (t80) REVERT: A 280 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.6221 (m-80) REVERT: A 401 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5450 (tp30) outliers start: 14 outliers final: 6 residues processed: 59 average time/residue: 0.0434 time to fit residues: 3.3657 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 : 0.067 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 0.0370 chunk 8 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 0.0020 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.3066 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.136705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.114090 restraints weight = 3524.951| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.75 r_work: 0.3315 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2108 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= 0.129 Angle : 0.586 10.691 4419 Z= 0.291 Chirality : 0.041 0.157 505 Planarity : 0.004 0.036 526 Dihedral : 9.399 156.391 439 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.70 % Allowed : 23.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.44), residues: 383 helix: 1.54 (0.29), residues: 322 sheet: None (None), residues: 0 loop : 0.78 (0.94), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.022 0.001 TYR A 280 PHE 0.022 0.001 PHE A 71 TRP 0.017 0.001 TRP A 94 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3231) covalent geometry : angle 0.58629 ( 4419) hydrogen bonds : bond 0.04256 ( 245) hydrogen bonds : angle 4.28666 ( 735) *********************** 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 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 151 TYR cc_start: 0.8300 (t80) cc_final: 0.8081 (t80) REVERT: A 280 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.6128 (m-80) REVERT: A 365 TYR cc_start: 0.8317 (m-80) cc_final: 0.8070 (m-80) REVERT: A 401 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5448 (tp30) outliers start: 9 outliers final: 5 residues processed: 56 average time/residue: 0.0486 time to fit residues: 3.6211 Evaluate side-chains 52 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 401 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.145799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.123930 restraints weight = 3473.465| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.68 r_work: 0.3319 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2093 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= 0.158 Angle : 0.609 11.149 4419 Z= 0.302 Chirality : 0.043 0.187 505 Planarity : 0.004 0.035 526 Dihedral : 9.317 156.236 439 Min Nonbonded Distance : 2.590 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.43), residues: 383 helix: 1.50 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 0.65 (0.92), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 402 TYR 0.022 0.001 TYR A 280 PHE 0.024 0.001 PHE A 71 TRP 0.019 0.002 TRP A 94 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3231) covalent geometry : angle 0.60888 ( 4419) hydrogen bonds : bond 0.04472 ( 245) hydrogen bonds : angle 4.39822 ( 735) *********************** 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 : 0.126 Fit side-chains revert: symmetry clash REVERT: A 280 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.6225 (m-80) REVERT: A 365 TYR cc_start: 0.8355 (m-80) cc_final: 0.8110 (m-80) REVERT: A 401 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.5413 (tp30) outliers start: 11 outliers final: 7 residues processed: 54 average time/residue: 0.0453 time to fit residues: 3.2424 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 : 0.106 ------------------------------------------------------------------------------- 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 129 SER 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 296 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 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.142584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120151 restraints weight = 3412.983| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.74 r_work: 0.3110 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3231 Z= 0.162 Angle : 0.606 11.246 4419 Z= 0.302 Chirality : 0.043 0.178 505 Planarity : 0.004 0.035 526 Dihedral : 9.228 155.032 439 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.78 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.43), residues: 383 helix: 1.55 (0.28), residues: 316 sheet: None (None), residues: 0 loop : 0.48 (0.88), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 402 TYR 0.022 0.001 TYR A 280 PHE 0.025 0.001 PHE A 71 TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 3231) covalent geometry : angle 0.60600 ( 4419) hydrogen bonds : bond 0.04479 ( 245) hydrogen bonds : angle 4.42675 ( 735) *********************** 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 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8285 (m-80) cc_final: 0.8020 (m-80) REVERT: A 401 GLU cc_start: 0.5817 (OUTLIER) cc_final: 0.5210 (tp30) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.0490 time to fit residues: 3.6766 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 : 0.119 ------------------------------------------------------------------------------- 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 129 SER 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 Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 8 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.144715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.123209 restraints weight = 3391.206| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.65 r_work: 0.3270 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.004 0.037 3231 Z= 0.154 Angle : 0.623 11.202 4419 Z= 0.305 Chirality : 0.042 0.170 505 Planarity : 0.004 0.035 526 Dihedral : 9.165 154.204 439 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.40 % Allowed : 24.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.43), residues: 383 helix: 1.57 (0.28), residues: 316 sheet: None (None), residues: 0 loop : 0.45 (0.88), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 402 TYR 0.022 0.001 TYR A 280 PHE 0.024 0.001 PHE A 71 TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3231) covalent geometry : angle 0.62257 ( 4419) hydrogen bonds : bond 0.04424 ( 245) hydrogen bonds : angle 4.41292 ( 735) ********************** 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: 8 poor density : 49 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8320 (m-80) cc_final: 0.8072 (m-80) REVERT: A 401 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5351 (tp30) outliers start: 8 outliers final: 7 residues processed: 55 average time/residue: 0.0407 time to fit residues: 2.9713 Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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 129 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.140996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118430 restraints weight = 3484.346| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.75 r_work: 0.3228 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2196 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= 0.153 Angle : 0.620 11.267 4419 Z= 0.304 Chirality : 0.042 0.167 505 Planarity : 0.004 0.036 526 Dihedral : 9.128 154.006 439 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 : 2.70 % Allowed : 23.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.43), residues: 383 helix: 1.59 (0.28), residues: 316 sheet: None (None), residues: 0 loop : 0.45 (0.88), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 402 TYR 0.022 0.001 TYR A 280 PHE 0.024 0.001 PHE A 71 TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 3231) covalent geometry : angle 0.61961 ( 4419) hydrogen bonds : bond 0.04410 ( 245) hydrogen bonds : angle 4.41636 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 946.45 seconds wall clock time: 17 minutes 1.82 seconds (1021.82 seconds total)