Starting phenix.real_space_refine on Thu Mar 6 01:45:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hff_34719/03_2025/8hff_34719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hff_34719/03_2025/8hff_34719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hff_34719/03_2025/8hff_34719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hff_34719/03_2025/8hff_34719.map" model { file = "/net/cci-nas-00/data/ceres_data/8hff_34719/03_2025/8hff_34719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hff_34719/03_2025/8hff_34719.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.127 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 20 5.16 5 C 2953 2.51 5 N 681 2.21 5 O 745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4399 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4373 Classifications: {'peptide': 547} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Unusual residues: {'LNR': 2} Classifications: {'undetermined': 2, 'water': 2} Link IDs: {None: 3} Time building chain proxies: 3.22, per 1000 atoms: 0.73 Number of scatterers: 4399 At special positions: 0 Unit cell: (70.3625, 69.28, 98.5075, 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 20 16.00 O 745 8.00 N 681 7.00 C 2953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 510.5 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 82.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.649A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.691A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.639A pdb=" N THR A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 261 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.817A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.906A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.714A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.968A pdb=" N TYR A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 385 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.615A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.796A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 497 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.587A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.507A pdb=" N ILE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 604 removed outlier: 4.040A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.759A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 302 hydrogen bonds defined for protein. 867 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: 1.14 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 649 1.29 - 1.42: 1370 1.42 - 1.55: 2488 1.55 - 1.68: 0 1.68 - 1.81: 31 Bond restraints: 4538 Sorted by residual: bond pdb=" C GLY A 92 " pdb=" O GLY A 92 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.35e-02 5.49e+03 2.98e+01 bond pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 1.232 1.167 0.065 1.36e-02 5.41e+03 2.31e+01 bond pdb=" C GLY A 92 " pdb=" N ALA A 93 " ideal model delta sigma weight residual 1.332 1.268 0.064 1.40e-02 5.10e+03 2.09e+01 bond pdb=" C GLY A 91 " pdb=" O GLY A 91 " ideal model delta sigma weight residual 1.235 1.186 0.048 1.35e-02 5.49e+03 1.28e+01 bond pdb=" C GLY A 90 " pdb=" O GLY A 90 " ideal model delta sigma weight residual 1.235 1.191 0.043 1.35e-02 5.49e+03 1.03e+01 ... (remaining 4533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 6006 1.31 - 2.61: 131 2.61 - 3.92: 40 3.92 - 5.22: 12 5.22 - 6.53: 1 Bond angle restraints: 6190 Sorted by residual: angle pdb=" CA ASN A 89 " pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 121.17 117.39 3.78 1.24e+00 6.50e-01 9.29e+00 angle pdb=" N GLY A 90 " pdb=" CA GLY A 90 " pdb=" C GLY A 90 " ideal model delta sigma weight residual 113.18 119.71 -6.53 2.37e+00 1.78e-01 7.59e+00 angle pdb=" C ASN A 89 " pdb=" CA ASN A 89 " pdb=" CB ASN A 89 " ideal model delta sigma weight residual 111.23 115.90 -4.67 1.70e+00 3.46e-01 7.53e+00 angle pdb=" C PHE A 150 " pdb=" N TYR A 151 " pdb=" CA TYR A 151 " ideal model delta sigma weight residual 121.14 116.53 4.61 1.75e+00 3.27e-01 6.93e+00 angle pdb=" CA TYR A 151 " pdb=" CB TYR A 151 " pdb=" CG TYR A 151 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.59e+00 ... (remaining 6185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 2209 17.79 - 35.58: 251 35.58 - 53.37: 61 53.37 - 71.16: 15 71.16 - 88.95: 1 Dihedral angle restraints: 2537 sinusoidal: 957 harmonic: 1580 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -131.34 8.74 0 2.50e+00 1.60e-01 1.22e+01 dihedral pdb=" CA ASP A 64 " pdb=" CB ASP A 64 " pdb=" CG ASP A 64 " pdb=" OD1 ASP A 64 " ideal model delta sinusoidal sigma weight residual -30.00 -89.91 59.91 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 2534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 633 0.067 - 0.135: 54 0.135 - 0.202: 3 0.202 - 0.270: 0 0.270 - 0.337: 1 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CAL LNR A 702 " pdb=" CAH LNR A 702 " pdb=" CAK LNR A 702 " pdb=" OAD LNR A 702 " both_signs ideal model delta sigma weight residual False -2.28 -2.43 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 688 not shown) Planarity restraints: 751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ILE A 103 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 89 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C ASN A 89 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN A 89 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY A 90 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 88 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C LYS A 88 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS A 88 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 89 " 0.017 2.00e-02 2.50e+03 ... (remaining 748 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 79 2.69 - 3.25: 4446 3.25 - 3.80: 7147 3.80 - 4.35: 9270 4.35 - 4.90: 16096 Nonbonded interactions: 37038 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" OG SER A 419 " model vdw 2.142 3.040 nonbonded pdb=" O ALA A 328 " pdb=" OG SER A 331 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASN A 337 " pdb=" N ASN A 338 " model vdw 2.287 3.120 nonbonded pdb=" O THR A 283 " pdb=" OG1 THR A 283 " model vdw 2.327 3.040 nonbonded pdb=" N ASP A 175 " pdb=" OD1 ASP A 175 " model vdw 2.367 3.120 ... (remaining 37033 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.940 Find NCS groups from input model: 0.040 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:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 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 : 0.004 0.074 4538 Z= 0.236 Angle : 0.544 6.527 6190 Z= 0.292 Chirality : 0.040 0.337 691 Planarity : 0.004 0.039 751 Dihedral : 16.022 88.952 1528 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.08 % Allowed : 19.52 % Favored : 79.39 % 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: 1.96 (0.38), residues: 543 helix: 1.68 (0.28), residues: 376 sheet: None (None), residues: 0 loop : 0.60 (0.53), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.001 0.000 HIS A 296 PHE 0.009 0.001 PHE A 362 TYR 0.018 0.001 TYR A 151 ARG 0.001 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.475 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 57 average time/residue: 0.7262 time to fit residues: 44.1944 Evaluate side-chains 54 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 498 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113843 restraints weight = 5203.138| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.99 r_work: 0.3173 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4538 Z= 0.231 Angle : 0.531 8.089 6190 Z= 0.277 Chirality : 0.040 0.150 691 Planarity : 0.004 0.047 751 Dihedral : 5.938 58.160 607 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.17 % Allowed : 16.49 % Favored : 81.34 % 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: 1.94 (0.38), residues: 543 helix: 1.69 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 0.47 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.016 0.001 PHE A 101 TYR 0.017 0.001 TYR A 84 ARG 0.002 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.456 Fit side-chains REVERT: A 329 PHE cc_start: 0.7801 (m-80) cc_final: 0.7464 (m-10) REVERT: A 459 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6480 (t80) outliers start: 10 outliers final: 2 residues processed: 55 average time/residue: 0.6107 time to fit residues: 36.3429 Evaluate side-chains 48 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114425 restraints weight = 5151.440| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.42 r_work: 0.3153 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4538 Z= 0.336 Angle : 0.570 9.335 6190 Z= 0.300 Chirality : 0.042 0.160 691 Planarity : 0.005 0.049 751 Dihedral : 5.531 52.420 602 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.04 % Allowed : 16.05 % Favored : 80.91 % 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: 1.61 (0.37), residues: 543 helix: 1.44 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.38 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 253 HIS 0.003 0.001 HIS A 280 PHE 0.013 0.002 PHE A 316 TYR 0.021 0.001 TYR A 84 ARG 0.002 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.7875 (m-80) cc_final: 0.7542 (m-10) REVERT: A 365 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6466 (pt) REVERT: A 459 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.6815 (t80) outliers start: 14 outliers final: 4 residues processed: 56 average time/residue: 0.6068 time to fit residues: 36.7602 Evaluate side-chains 47 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.149017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114912 restraints weight = 5245.022| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.97 r_work: 0.3155 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4538 Z= 0.213 Angle : 0.506 7.491 6190 Z= 0.268 Chirality : 0.040 0.147 691 Planarity : 0.004 0.050 751 Dihedral : 5.083 46.123 602 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.60 % Allowed : 17.57 % Favored : 79.83 % 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: 1.82 (0.37), residues: 543 helix: 1.59 (0.27), residues: 385 sheet: None (None), residues: 0 loop : 0.43 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.012 0.001 PHE A 110 TYR 0.016 0.001 TYR A 84 ARG 0.002 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.7876 (m-80) cc_final: 0.7561 (m-10) REVERT: A 371 GLU cc_start: 0.7859 (tp30) cc_final: 0.7210 (tt0) REVERT: A 459 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.6520 (t80) REVERT: A 509 MET cc_start: 0.8183 (mtm) cc_final: 0.7689 (mtm) outliers start: 12 outliers final: 3 residues processed: 53 average time/residue: 0.6577 time to fit residues: 37.4739 Evaluate side-chains 46 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110833 restraints weight = 5311.723| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.07 r_work: 0.3169 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4538 Z= 0.198 Angle : 0.493 7.332 6190 Z= 0.260 Chirality : 0.039 0.151 691 Planarity : 0.004 0.051 751 Dihedral : 4.852 40.501 602 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.17 % Allowed : 18.66 % Favored : 79.18 % 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: 1.99 (0.37), residues: 543 helix: 1.74 (0.27), residues: 384 sheet: None (None), residues: 0 loop : 0.43 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.002 0.000 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8334 (m110) cc_final: 0.7850 (m110) REVERT: A 274 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6859 (tp) REVERT: A 329 PHE cc_start: 0.7697 (m-80) cc_final: 0.7386 (m-10) REVERT: A 371 GLU cc_start: 0.7749 (tp30) cc_final: 0.7029 (tt0) REVERT: A 459 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.6449 (t80) REVERT: A 509 MET cc_start: 0.8067 (mtm) cc_final: 0.7572 (mtm) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 0.6736 time to fit residues: 39.0104 Evaluate side-chains 48 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 0.0670 chunk 53 optimal weight: 0.0010 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.0020 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.3532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.155116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121175 restraints weight = 5199.994| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.03 r_work: 0.3247 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4538 Z= 0.149 Angle : 0.462 5.993 6190 Z= 0.244 Chirality : 0.038 0.137 691 Planarity : 0.004 0.052 751 Dihedral : 4.494 36.272 602 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.74 % Allowed : 20.17 % Favored : 78.09 % 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: 2.19 (0.37), residues: 543 helix: 1.87 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.57 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.001 0.000 HIS A 613 PHE 0.011 0.001 PHE A 110 TYR 0.015 0.001 TYR A 151 ARG 0.001 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8260 (m110) cc_final: 0.8039 (m110) REVERT: A 329 PHE cc_start: 0.7755 (m-80) cc_final: 0.7449 (m-10) REVERT: A 371 GLU cc_start: 0.7747 (tp30) cc_final: 0.7129 (tt0) outliers start: 8 outliers final: 2 residues processed: 56 average time/residue: 0.6964 time to fit residues: 41.8369 Evaluate side-chains 47 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.0870 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119063 restraints weight = 5201.747| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.97 r_work: 0.3217 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4538 Z= 0.184 Angle : 0.479 7.136 6190 Z= 0.252 Chirality : 0.039 0.147 691 Planarity : 0.004 0.051 751 Dihedral : 4.377 31.785 600 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.74 % Allowed : 20.82 % Favored : 77.44 % 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: 2.13 (0.37), residues: 543 helix: 1.85 (0.27), residues: 387 sheet: None (None), residues: 0 loop : 0.45 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.002 0.000 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.016 0.001 TYR A 151 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.424 Fit side-chains REVERT: A 78 ASN cc_start: 0.8302 (m110) cc_final: 0.8065 (m110) REVERT: A 329 PHE cc_start: 0.7828 (m-80) cc_final: 0.7522 (m-10) REVERT: A 371 GLU cc_start: 0.7804 (tp30) cc_final: 0.7141 (tt0) REVERT: A 459 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6502 (t80) outliers start: 8 outliers final: 5 residues processed: 50 average time/residue: 0.6516 time to fit residues: 35.0884 Evaluate side-chains 47 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.151054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117097 restraints weight = 5213.253| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.99 r_work: 0.3194 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4538 Z= 0.201 Angle : 0.488 7.424 6190 Z= 0.256 Chirality : 0.039 0.153 691 Planarity : 0.004 0.052 751 Dihedral : 4.445 32.523 600 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.95 % Allowed : 20.61 % Favored : 77.44 % 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: 2.07 (0.37), residues: 543 helix: 1.80 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.44 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 235 HIS 0.002 0.000 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 2.131 Fit side-chains REVERT: A 78 ASN cc_start: 0.8329 (m110) cc_final: 0.8058 (m110) REVERT: A 329 PHE cc_start: 0.7825 (m-80) cc_final: 0.7516 (m-10) REVERT: A 371 GLU cc_start: 0.7826 (tp30) cc_final: 0.7167 (tt0) REVERT: A 459 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6624 (t80) outliers start: 9 outliers final: 5 residues processed: 52 average time/residue: 1.6425 time to fit residues: 90.8168 Evaluate side-chains 49 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 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 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.152179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118516 restraints weight = 5258.866| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.99 r_work: 0.3215 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4538 Z= 0.185 Angle : 0.478 6.785 6190 Z= 0.250 Chirality : 0.039 0.149 691 Planarity : 0.004 0.052 751 Dihedral : 4.369 31.692 600 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.74 % Allowed : 21.26 % Favored : 77.01 % 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: 2.08 (0.37), residues: 543 helix: 1.84 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.35 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.016 0.001 TYR A 151 ARG 0.001 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.610 Fit side-chains REVERT: A 78 ASN cc_start: 0.8301 (m110) cc_final: 0.8050 (m110) REVERT: A 329 PHE cc_start: 0.7814 (m-80) cc_final: 0.7507 (m-10) REVERT: A 371 GLU cc_start: 0.7812 (tp30) cc_final: 0.7173 (tt0) REVERT: A 459 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.6572 (t80) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 1.1365 time to fit residues: 60.7347 Evaluate side-chains 49 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115998 restraints weight = 5204.947| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.98 r_work: 0.3178 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4538 Z= 0.221 Angle : 0.502 7.698 6190 Z= 0.263 Chirality : 0.039 0.153 691 Planarity : 0.004 0.052 751 Dihedral : 4.522 33.404 600 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.52 % Allowed : 21.48 % Favored : 77.01 % 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 (0.37), residues: 543 helix: 1.71 (0.27), residues: 388 sheet: None (None), residues: 0 loop : 0.38 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 235 HIS 0.003 0.000 HIS A 280 PHE 0.010 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.499 Fit side-chains REVERT: A 78 ASN cc_start: 0.8344 (m110) cc_final: 0.8063 (m110) REVERT: A 329 PHE cc_start: 0.7823 (m-80) cc_final: 0.7500 (m-10) REVERT: A 371 GLU cc_start: 0.7817 (tp30) cc_final: 0.7161 (tt0) REVERT: A 459 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.6609 (t80) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.7358 time to fit residues: 37.8639 Evaluate side-chains 47 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 0.0270 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 6 optimal weight: 0.1980 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121784 restraints weight = 5232.962| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.03 r_work: 0.3278 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4538 Z= 0.144 Angle : 0.453 5.320 6190 Z= 0.239 Chirality : 0.038 0.132 691 Planarity : 0.004 0.051 751 Dihedral : 4.099 28.658 600 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.30 % Allowed : 21.69 % Favored : 77.01 % 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: 2.22 (0.38), residues: 543 helix: 1.91 (0.27), residues: 388 sheet: None (None), residues: 0 loop : 0.51 (0.56), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 553 HIS 0.001 0.000 HIS A 613 PHE 0.017 0.001 PHE A 164 TYR 0.013 0.001 TYR A 151 ARG 0.001 0.000 ARG A 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3406.76 seconds wall clock time: 61 minutes 38.16 seconds (3698.16 seconds total)