Starting phenix.real_space_refine on Sat Apr 26 18:40:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7t_39827/04_2025/8z7t_39827.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7t_39827/04_2025/8z7t_39827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7t_39827/04_2025/8z7t_39827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7t_39827/04_2025/8z7t_39827.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7t_39827/04_2025/8z7t_39827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7t_39827/04_2025/8z7t_39827.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2099 2.51 5 N 464 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 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3110 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: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UEG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.67, per 1000 atoms: 0.86 Number of scatterers: 3110 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 15 16.00 O 532 8.00 N 464 7.00 C 2099 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: 0.80 Conformation dependent library (CDL) restraints added in 367.9 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.586A pdb=" N ASN A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.727A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 4.373A pdb=" N VAL A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 99 removed outlier: 3.661A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 131 removed outlier: 4.323A pdb=" N THR A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.513A 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 164 Processing helix chain 'A' and resid 168 through 189 Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.569A pdb=" N PHE A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 307 removed outlier: 4.232A pdb=" N TRP A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 337 removed outlier: 4.222A pdb=" N TYR A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 366 Processing helix chain 'A' and resid 368 through 398 Processing helix chain 'A' and resid 402 through 426 removed outlier: 3.528A pdb=" N VAL A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 461 removed outlier: 3.720A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (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: 0.85 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 890 1.35 - 1.47: 936 1.47 - 1.59: 1351 1.59 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 3203 Sorted by residual: bond pdb=" C3 UEG A 501 " pdb=" O3 UEG A 501 " ideal model delta sigma weight residual 1.348 1.401 -0.053 2.00e-02 2.50e+03 7.12e+00 bond pdb=" N ARG A 429 " pdb=" CA ARG A 429 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.33e-02 5.65e+03 5.57e+00 bond pdb=" C4 UEG A 501 " pdb=" C5 UEG A 501 " ideal model delta sigma weight residual 1.399 1.355 0.044 2.00e-02 2.50e+03 4.81e+00 bond pdb=" C3 UEG A 501 " pdb=" C4 UEG A 501 " ideal model delta sigma weight residual 1.392 1.354 0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C2 UEG A 501 " pdb=" N1 UEG A 501 " ideal model delta sigma weight residual 1.322 1.352 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 3198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 4329 2.37 - 4.74: 41 4.74 - 7.11: 6 7.11 - 9.48: 1 9.48 - 11.86: 1 Bond angle restraints: 4378 Sorted by residual: angle pdb=" CB MET A 455 " pdb=" CG MET A 455 " pdb=" SD MET A 455 " ideal model delta sigma weight residual 112.70 124.56 -11.86 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CA TYR A 280 " pdb=" CB TYR A 280 " pdb=" CG TYR A 280 " ideal model delta sigma weight residual 113.90 119.08 -5.18 1.80e+00 3.09e-01 8.27e+00 angle pdb=" CA LYS A 276 " pdb=" CB LYS A 276 " pdb=" CG LYS A 276 " ideal model delta sigma weight residual 114.10 119.21 -5.11 2.00e+00 2.50e-01 6.54e+00 angle pdb=" N ARG A 429 " pdb=" CA ARG A 429 " pdb=" C ARG A 429 " ideal model delta sigma weight residual 112.54 109.54 3.00 1.22e+00 6.72e-01 6.06e+00 angle pdb=" CB MET A 106 " pdb=" CG MET A 106 " pdb=" SD MET A 106 " ideal model delta sigma weight residual 112.70 119.93 -7.23 3.00e+00 1.11e-01 5.81e+00 ... (remaining 4373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 1533 16.92 - 33.83: 212 33.83 - 50.75: 53 50.75 - 67.67: 8 67.67 - 84.58: 4 Dihedral angle restraints: 1810 sinusoidal: 661 harmonic: 1149 Sorted by residual: dihedral pdb=" CG ARG A 429 " pdb=" CD ARG A 429 " pdb=" NE ARG A 429 " pdb=" CZ ARG A 429 " ideal model delta sinusoidal sigma weight residual -90.00 -34.77 -55.23 2 1.50e+01 4.44e-03 1.44e+01 dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" N LEU A 67 " pdb=" CA LEU A 67 " pdb=" CB LEU A 67 " pdb=" CG LEU A 67 " ideal model delta sinusoidal sigma weight residual -60.00 -115.48 55.48 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 1807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 300 0.028 - 0.056: 115 0.056 - 0.085: 62 0.085 - 0.113: 24 0.113 - 0.141: 4 Chirality restraints: 505 Sorted by residual: chirality pdb=" CB ILE A 175 " pdb=" CA ILE A 175 " pdb=" CG1 ILE A 175 " pdb=" CG2 ILE A 175 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.97e-01 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 2.38 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL A 400 " pdb=" N VAL A 400 " pdb=" C VAL A 400 " pdb=" CB VAL A 400 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 502 not shown) Planarity restraints: 524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 36 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO A 37 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 37 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 37 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 141 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C GLY A 141 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY A 141 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR A 142 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 143 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C CYS A 143 " -0.034 2.00e-02 2.50e+03 pdb=" O CYS A 143 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 144 " 0.012 2.00e-02 2.50e+03 ... (remaining 521 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 384 2.75 - 3.28: 3392 3.28 - 3.82: 5604 3.82 - 4.36: 6269 4.36 - 4.90: 10810 Nonbonded interactions: 26459 Sorted by model distance: nonbonded pdb=" OD1 ASN A 356 " pdb=" OG SER A 382 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR A 289 " pdb=" OH TYR A 383 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR A 273 " pdb=" OD1 ASN A 410 " model vdw 2.262 3.040 nonbonded pdb=" O ALA A 49 " pdb=" ND2 ASN A 53 " model vdw 2.265 3.120 nonbonded pdb=" O VAL A 70 " pdb=" OG1 THR A 74 " model vdw 2.267 3.040 ... (remaining 26454 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: 1.020 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.480 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.003 0.053 3203 Z= 0.176 Angle : 0.622 11.855 4378 Z= 0.325 Chirality : 0.041 0.141 505 Planarity : 0.006 0.050 524 Dihedral : 16.891 84.584 1076 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.60 % Allowed : 26.13 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.43), residues: 383 helix: 0.39 (0.29), residues: 305 sheet: None (None), residues: 0 loop : 0.46 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.012 0.001 PHE A 71 TYR 0.013 0.001 TYR A 383 ARG 0.003 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.18290 ( 245) hydrogen bonds : angle 7.18642 ( 735) covalent geometry : bond 0.00349 ( 3203) covalent geometry : angle 0.62216 ( 4378) *********************** 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 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7862 (mm110) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.1784 time to fit residues: 11.3279 Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.140802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111590 restraints weight = 3532.675| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.74 r_work: 0.3104 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3203 Z= 0.162 Angle : 0.606 6.857 4378 Z= 0.317 Chirality : 0.043 0.199 505 Planarity : 0.005 0.042 524 Dihedral : 6.044 81.257 427 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.50 % Allowed : 24.32 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.44), residues: 383 helix: 1.12 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 1.04 (0.88), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.001 0.000 HIS A 135 PHE 0.015 0.001 PHE A 439 TYR 0.013 0.002 TYR A 383 ARG 0.003 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.05229 ( 245) hydrogen bonds : angle 4.59022 ( 735) covalent geometry : bond 0.00356 ( 3203) covalent geometry : angle 0.60616 ( 4378) *********************** 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 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7863 (mm-30) REVERT: A 368 ASN cc_start: 0.7731 (p0) cc_final: 0.7445 (p0) outliers start: 5 outliers final: 1 residues processed: 59 average time/residue: 0.1515 time to fit residues: 11.4002 Evaluate side-chains 51 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 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 86 GLN ** 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 = 0.3540 r_free = 0.3540 target = 0.141144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.111973 restraints weight = 3478.149| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.74 r_work: 0.3076 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3203 Z= 0.162 Angle : 0.589 6.047 4378 Z= 0.307 Chirality : 0.043 0.211 505 Planarity : 0.004 0.046 524 Dihedral : 5.527 75.034 425 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.30 % Allowed : 24.32 % Favored : 72.37 % 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: 1.66 (0.43), residues: 383 helix: 1.21 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 1.04 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.017 0.001 PHE A 439 TYR 0.014 0.002 TYR A 383 ARG 0.001 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04995 ( 245) hydrogen bonds : angle 4.34063 ( 735) covalent geometry : bond 0.00365 ( 3203) covalent geometry : angle 0.58920 ( 4378) *********************** 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 64 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASN cc_start: 0.7654 (p0) cc_final: 0.7359 (p0) outliers start: 11 outliers final: 4 residues processed: 62 average time/residue: 0.1317 time to fit residues: 10.4147 Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 423 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.143247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.114298 restraints weight = 3517.572| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.75 r_work: 0.3056 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3203 Z= 0.170 Angle : 0.627 9.953 4378 Z= 0.320 Chirality : 0.044 0.214 505 Planarity : 0.004 0.047 524 Dihedral : 5.682 79.090 425 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.60 % Allowed : 25.23 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.43), residues: 383 helix: 1.24 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 0.65 (0.87), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.017 0.001 PHE A 439 TYR 0.015 0.002 TYR A 383 ARG 0.001 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 245) hydrogen bonds : angle 4.27122 ( 735) covalent geometry : bond 0.00390 ( 3203) covalent geometry : angle 0.62681 ( 4378) *********************** 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 61 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8462 (tmm) cc_final: 0.7980 (tmm) REVERT: A 368 ASN cc_start: 0.7626 (p0) cc_final: 0.7343 (p0) outliers start: 12 outliers final: 7 residues processed: 59 average time/residue: 0.1169 time to fit residues: 9.0523 Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 423 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.133951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.107514 restraints weight = 3607.693| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.46 r_work: 0.2973 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3203 Z= 0.152 Angle : 0.611 11.460 4378 Z= 0.306 Chirality : 0.043 0.210 505 Planarity : 0.004 0.046 524 Dihedral : 5.433 73.163 425 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.60 % Allowed : 24.32 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.43), residues: 383 helix: 1.28 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.65 (0.87), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.015 0.001 PHE A 439 TYR 0.015 0.001 TYR A 383 ARG 0.001 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 245) hydrogen bonds : angle 4.19108 ( 735) covalent geometry : bond 0.00342 ( 3203) covalent geometry : angle 0.61056 ( 4378) *********************** 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 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8750 (mt) cc_final: 0.8463 (mp) REVERT: A 368 ASN cc_start: 0.7475 (p0) cc_final: 0.7188 (p0) REVERT: A 458 MET cc_start: 0.7622 (tpt) cc_final: 0.7293 (ptp) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 0.1165 time to fit residues: 9.2810 Evaluate side-chains 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.0000 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.147383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118823 restraints weight = 3503.665| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.76 r_work: 0.3091 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3203 Z= 0.135 Angle : 0.593 11.413 4378 Z= 0.295 Chirality : 0.042 0.213 505 Planarity : 0.004 0.044 524 Dihedral : 5.236 68.428 425 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.60 % Allowed : 24.62 % Favored : 71.77 % 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: 1.79 (0.43), residues: 383 helix: 1.35 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.71 (0.87), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.011 0.001 PHE A 71 TYR 0.015 0.001 TYR A 383 ARG 0.001 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 245) hydrogen bonds : angle 4.07880 ( 735) covalent geometry : bond 0.00293 ( 3203) covalent geometry : angle 0.59299 ( 4378) *********************** 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 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8672 (mt) cc_final: 0.8379 (mp) REVERT: A 368 ASN cc_start: 0.7360 (p0) cc_final: 0.7070 (p0) REVERT: A 458 MET cc_start: 0.7529 (tpt) cc_final: 0.7157 (ptp) outliers start: 12 outliers final: 7 residues processed: 61 average time/residue: 0.1317 time to fit residues: 10.5290 Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.143934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.114233 restraints weight = 3506.696| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.82 r_work: 0.2995 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3203 Z= 0.156 Angle : 0.612 10.001 4378 Z= 0.307 Chirality : 0.043 0.205 505 Planarity : 0.004 0.045 524 Dihedral : 5.076 61.063 425 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.00 % Allowed : 25.23 % Favored : 71.77 % 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: 1.79 (0.43), residues: 383 helix: 1.34 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.82 (0.87), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.013 0.001 PHE A 71 TYR 0.015 0.002 TYR A 383 ARG 0.001 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 245) hydrogen bonds : angle 4.13866 ( 735) covalent geometry : bond 0.00359 ( 3203) covalent geometry : angle 0.61199 ( 4378) *********************** 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 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8706 (mt) cc_final: 0.8404 (mp) REVERT: A 368 ASN cc_start: 0.7412 (p0) cc_final: 0.7141 (p0) REVERT: A 458 MET cc_start: 0.7513 (tpt) cc_final: 0.7137 (ptp) outliers start: 10 outliers final: 8 residues processed: 60 average time/residue: 0.1132 time to fit residues: 8.8818 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 : 0.330 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0070 chunk 35 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.145714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.117019 restraints weight = 3463.990| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.73 r_work: 0.2973 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3203 Z= 0.159 Angle : 0.627 9.152 4378 Z= 0.312 Chirality : 0.044 0.215 505 Planarity : 0.004 0.045 524 Dihedral : 4.979 56.139 425 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.00 % Allowed : 25.23 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.43), residues: 383 helix: 1.35 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.71 (0.85), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.014 0.001 PHE A 71 TYR 0.015 0.002 TYR A 383 ARG 0.000 0.000 ARG A 456 Details of bonding type rmsd hydrogen bonds : bond 0.04679 ( 245) hydrogen bonds : angle 4.15947 ( 735) covalent geometry : bond 0.00368 ( 3203) covalent geometry : angle 0.62729 ( 4378) *********************** 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: 10 poor density : 46 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8654 (mt) cc_final: 0.8336 (mp) REVERT: A 458 MET cc_start: 0.7483 (tpt) cc_final: 0.7111 (ptp) outliers start: 10 outliers final: 9 residues processed: 56 average time/residue: 0.1162 time to fit residues: 8.4507 Evaluate side-chains 54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.132334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.104829 restraints weight = 3634.307| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.55 r_work: 0.2929 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3203 Z= 0.175 Angle : 0.642 8.632 4378 Z= 0.321 Chirality : 0.045 0.221 505 Planarity : 0.004 0.045 524 Dihedral : 4.866 49.467 425 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.00 % Allowed : 25.83 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.43), residues: 383 helix: 1.33 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.72 (0.86), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.015 0.001 PHE A 71 TYR 0.015 0.002 TYR A 383 ARG 0.001 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04810 ( 245) hydrogen bonds : angle 4.22586 ( 735) covalent geometry : bond 0.00409 ( 3203) covalent geometry : angle 0.64196 ( 4378) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8784 (mt) cc_final: 0.8472 (mp) REVERT: A 458 MET cc_start: 0.7434 (tpt) cc_final: 0.7213 (ptp) outliers start: 10 outliers final: 10 residues processed: 55 average time/residue: 0.1170 time to fit residues: 8.3552 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 : 0.339 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.0010 chunk 14 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.134808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.107623 restraints weight = 3573.649| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.55 r_work: 0.2980 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3203 Z= 0.149 Angle : 0.624 9.174 4378 Z= 0.309 Chirality : 0.043 0.229 505 Planarity : 0.004 0.046 524 Dihedral : 4.591 39.408 425 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.60 % Allowed : 24.62 % Favored : 71.77 % 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: 1.84 (0.43), residues: 383 helix: 1.39 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.71 (0.86), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.013 0.001 PHE A 71 TYR 0.016 0.001 TYR A 383 ARG 0.000 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 245) hydrogen bonds : angle 4.13665 ( 735) covalent geometry : bond 0.00339 ( 3203) covalent geometry : angle 0.62413 ( 4378) ********************** 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 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8754 (mt) cc_final: 0.8454 (mp) REVERT: A 458 MET cc_start: 0.7418 (tpt) cc_final: 0.7191 (ptp) outliers start: 12 outliers final: 10 residues processed: 56 average time/residue: 0.1214 time to fit residues: 8.8324 Evaluate side-chains 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 32 optimal weight: 0.0980 chunk 7 optimal weight: 0.3980 chunk 26 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.3278 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.150563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122427 restraints weight = 3435.394| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.74 r_work: 0.3107 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3203 Z= 0.132 Angle : 0.619 9.702 4378 Z= 0.301 Chirality : 0.042 0.231 505 Planarity : 0.004 0.045 524 Dihedral : 4.205 20.423 425 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.40 % Allowed : 26.13 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.43), residues: 383 helix: 1.52 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.86 (0.89), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.010 0.001 PHE A 71 TYR 0.016 0.001 TYR A 383 ARG 0.000 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 245) hydrogen bonds : angle 4.01703 ( 735) covalent geometry : bond 0.00289 ( 3203) covalent geometry : angle 0.61921 ( 4378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2002.12 seconds wall clock time: 35 minutes 3.43 seconds (2103.43 seconds total)