Starting phenix.real_space_refine on Mon Feb 10 22:29:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7w_39830/02_2025/8z7w_39830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7w_39830/02_2025/8z7w_39830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7w_39830/02_2025/8z7w_39830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7w_39830/02_2025/8z7w_39830.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7w_39830/02_2025/8z7w_39830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7w_39830/02_2025/8z7w_39830.cif" } resolution = 3.09 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= 0.001 sd= 0.103 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 2095 2.51 5 N 468 2.21 5 O 529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3107 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: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.52, per 1000 atoms: 0.81 Number of scatterers: 3107 At special positions: 0 Unit cell: (64, 68, 71, 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 529 8.00 N 468 7.00 C 2095 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: 0.84 Conformation dependent library (CDL) restraints added in 393.6 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: 17 helices and 0 sheets defined 87.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 32 through 36 removed outlier: 3.553A pdb=" N LEU A 35 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE A 36 " --> pdb=" O PRO A 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 32 through 36' Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.729A pdb=" N SER A 40 " --> pdb=" O PRO A 37 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 41 " --> pdb=" O TYR A 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 37 through 41' Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.626A pdb=" N THR A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 53' Processing helix chain 'A' and resid 55 through 73 removed outlier: 4.019A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.864A pdb=" N VAL A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 99 removed outlier: 3.590A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 131 removed outlier: 3.502A pdb=" N MET A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.453A 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 274 Processing helix chain 'A' and resid 280 through 307 removed outlier: 4.286A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 337 removed outlier: 4.446A pdb=" N GLY A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 366 removed outlier: 3.720A pdb=" N LEU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 398 Processing helix chain 'A' and resid 402 through 426 Processing helix chain 'A' and resid 434 through 461 removed outlier: 3.913A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 720 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: 0.88 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 449 1.30 - 1.43: 966 1.43 - 1.56: 1758 1.56 - 1.69: 0 1.69 - 1.82: 26 Bond restraints: 3199 Sorted by residual: bond pdb=" C ALA A 447 " pdb=" O ALA A 447 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.18e-02 7.18e+03 3.75e+01 bond pdb=" C ALA A 450 " pdb=" O ALA A 450 " ideal model delta sigma weight residual 1.237 1.166 0.071 1.17e-02 7.31e+03 3.66e+01 bond pdb=" C PRO A 69 " pdb=" O PRO A 69 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.30e-02 5.92e+03 2.18e+01 bond pdb=" C ALA A 321 " pdb=" O ALA A 321 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.22e-02 6.72e+03 2.14e+01 bond pdb=" C TYR A 315 " pdb=" O TYR A 315 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.17e-02 7.31e+03 1.72e+01 ... (remaining 3194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 4159 2.21 - 4.41: 173 4.41 - 6.62: 29 6.62 - 8.83: 6 8.83 - 11.04: 5 Bond angle restraints: 4372 Sorted by residual: angle pdb=" N LEU A 35 " pdb=" CA LEU A 35 " pdb=" C LEU A 35 " ideal model delta sigma weight residual 112.04 102.68 9.36 1.44e+00 4.82e-01 4.23e+01 angle pdb=" N ALA A 447 " pdb=" CA ALA A 447 " pdb=" C ALA A 447 " ideal model delta sigma weight residual 111.33 104.22 7.11 1.21e+00 6.83e-01 3.46e+01 angle pdb=" CB GLU A 320 " pdb=" CG GLU A 320 " pdb=" CD GLU A 320 " ideal model delta sigma weight residual 112.60 122.33 -9.73 1.70e+00 3.46e-01 3.27e+01 angle pdb=" C ASN A 45 " pdb=" CA ASN A 45 " pdb=" CB ASN A 45 " ideal model delta sigma weight residual 111.80 119.94 -8.14 1.46e+00 4.69e-01 3.11e+01 angle pdb=" C THR A 47 " pdb=" CA THR A 47 " pdb=" CB THR A 47 " ideal model delta sigma weight residual 109.76 120.80 -11.04 1.99e+00 2.53e-01 3.08e+01 ... (remaining 4367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 1504 16.33 - 32.67: 222 32.67 - 49.00: 59 49.00 - 65.33: 20 65.33 - 81.66: 3 Dihedral angle restraints: 1808 sinusoidal: 659 harmonic: 1149 Sorted by residual: dihedral pdb=" C ASN A 45 " pdb=" N ASN A 45 " pdb=" CA ASN A 45 " pdb=" CB ASN A 45 " ideal model delta harmonic sigma weight residual -122.60 -142.73 20.13 0 2.50e+00 1.60e-01 6.48e+01 dihedral pdb=" N ASN A 45 " pdb=" C ASN A 45 " pdb=" CA ASN A 45 " pdb=" CB ASN A 45 " ideal model delta harmonic sigma weight residual 122.80 141.30 -18.50 0 2.50e+00 1.60e-01 5.48e+01 dihedral pdb=" C THR A 47 " pdb=" N THR A 47 " pdb=" CA THR A 47 " pdb=" CB THR A 47 " ideal model delta harmonic sigma weight residual -122.00 -133.88 11.88 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 1805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 484 0.151 - 0.301: 18 0.301 - 0.452: 2 0.452 - 0.603: 0 0.603 - 0.753: 1 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA ASN A 45 " pdb=" N ASN A 45 " pdb=" C ASN A 45 " pdb=" CB ASN A 45 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA LEU A 46 " pdb=" N LEU A 46 " pdb=" C LEU A 46 " pdb=" CB LEU A 46 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ILE A 449 " pdb=" N ILE A 449 " pdb=" C ILE A 449 " pdb=" CB ILE A 449 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 502 not shown) Planarity restraints: 524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 501 " -0.438 2.00e-02 2.50e+03 3.18e-01 2.27e+03 pdb=" C03 MF8 A 501 " 0.491 2.00e-02 2.50e+03 pdb=" C04 MF8 A 501 " -0.007 2.00e-02 2.50e+03 pdb=" C07 MF8 A 501 " -0.015 2.00e-02 2.50e+03 pdb=" N02 MF8 A 501 " 0.013 2.00e-02 2.50e+03 pdb=" N05 MF8 A 501 " -0.000 2.00e-02 2.50e+03 pdb=" N06 MF8 A 501 " -0.032 2.00e-02 2.50e+03 pdb=" N08 MF8 A 501 " -0.492 2.00e-02 2.50e+03 pdb=" N09 MF8 A 501 " 0.481 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 69 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PRO A 69 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO A 69 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 70 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 70 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C VAL A 70 " -0.048 2.00e-02 2.50e+03 pdb=" O VAL A 70 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE A 71 " 0.017 2.00e-02 2.50e+03 ... (remaining 521 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 699 2.77 - 3.30: 3279 3.30 - 3.84: 5570 3.84 - 4.37: 6550 4.37 - 4.90: 11132 Nonbonded interactions: 27230 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" OH TYR A 79 " model vdw 2.241 3.040 nonbonded pdb=" OE1 GLN A 294 " pdb=" OH TYR A 442 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A 128 " pdb=" OG SER A 140 " model vdw 2.257 3.040 nonbonded pdb=" O PHE A 287 " pdb=" OH TYR A 445 " model vdw 2.319 3.040 nonbonded pdb=" OH TYR A 126 " pdb=" O PRO A 191 " model vdw 2.325 3.040 ... (remaining 27225 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: 0.690 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.007 0.072 3199 Z= 0.467 Angle : 1.027 11.035 4372 Z= 0.687 Chirality : 0.070 0.753 505 Planarity : 0.015 0.318 524 Dihedral : 17.007 81.664 1074 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.30 % Allowed : 25.83 % Favored : 70.87 % Cbeta Deviations : 0.82 % 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: -0.06 (0.43), residues: 383 helix: 0.09 (0.28), residues: 318 sheet: None (None), residues: 0 loop : 0.09 (0.88), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.031 0.002 PHE A 279 TYR 0.017 0.002 TYR A 459 ARG 0.003 0.000 ARG A 456 *********************** 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 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.336 Fit side-chains REVERT: A 280 TYR cc_start: 0.8306 (t80) cc_final: 0.7886 (t80) REVERT: A 340 ASN cc_start: 0.8034 (p0) cc_final: 0.7305 (t0) outliers start: 11 outliers final: 4 residues processed: 52 average time/residue: 0.1739 time to fit residues: 11.0100 Evaluate side-chains 45 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 454 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113908 restraints weight = 3746.905| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.58 r_work: 0.3124 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3199 Z= 0.279 Angle : 0.666 8.978 4372 Z= 0.348 Chirality : 0.044 0.219 505 Planarity : 0.005 0.033 524 Dihedral : 5.067 31.535 429 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.00 % Allowed : 25.53 % 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: 1.20 (0.43), residues: 383 helix: 0.96 (0.29), residues: 325 sheet: None (None), residues: 0 loop : 0.44 (0.89), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.004 0.001 HIS A 364 PHE 0.023 0.002 PHE A 71 TYR 0.014 0.002 TYR A 280 ARG 0.001 0.000 ARG A 456 *********************** 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 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.362 Fit side-chains REVERT: A 120 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6410 (pt0) REVERT: A 146 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8369 (t) REVERT: A 265 TRP cc_start: 0.7971 (t60) cc_final: 0.7615 (t60) REVERT: A 315 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.6905 (t80) REVERT: A 340 ASN cc_start: 0.8169 (p0) cc_final: 0.7119 (t0) REVERT: A 385 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8150 (tp) outliers start: 10 outliers final: 3 residues processed: 57 average time/residue: 0.1126 time to fit residues: 8.6304 Evaluate side-chains 49 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.154582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135042 restraints weight = 3487.284| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.56 r_work: 0.3453 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3199 Z= 0.240 Angle : 0.616 9.528 4372 Z= 0.317 Chirality : 0.042 0.215 505 Planarity : 0.004 0.035 524 Dihedral : 4.352 19.641 423 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.50 % Allowed : 23.42 % 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: 1.42 (0.43), residues: 383 helix: 1.13 (0.28), residues: 327 sheet: None (None), residues: 0 loop : 0.37 (0.91), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.016 0.001 PHE A 71 TYR 0.013 0.002 TYR A 298 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.333 Fit side-chains REVERT: A 120 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6746 (pt0) REVERT: A 146 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8500 (t) REVERT: A 265 TRP cc_start: 0.8302 (t60) cc_final: 0.7939 (t60) REVERT: A 280 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.6506 (m-80) REVERT: A 315 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7079 (t80) REVERT: A 340 ASN cc_start: 0.8362 (p0) cc_final: 0.7251 (t0) REVERT: A 385 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8300 (tp) outliers start: 15 outliers final: 8 residues processed: 53 average time/residue: 0.1059 time to fit residues: 7.5037 Evaluate side-chains 54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.153586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132941 restraints weight = 3541.206| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.69 r_work: 0.3402 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3199 Z= 0.211 Angle : 0.588 9.837 4372 Z= 0.303 Chirality : 0.041 0.199 505 Planarity : 0.004 0.034 524 Dihedral : 4.246 19.728 423 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 5.71 % Allowed : 22.82 % 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: 1.61 (0.43), residues: 383 helix: 1.27 (0.29), residues: 324 sheet: None (None), residues: 0 loop : 0.34 (0.92), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 71 TYR 0.013 0.001 TYR A 128 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6714 (pt0) REVERT: A 146 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8474 (t) REVERT: A 265 TRP cc_start: 0.8335 (t60) cc_final: 0.8020 (t60) REVERT: A 280 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.6542 (m-80) REVERT: A 340 ASN cc_start: 0.8360 (p0) cc_final: 0.7306 (t0) REVERT: A 385 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8287 (tp) REVERT: A 452 ILE cc_start: 0.7615 (mt) cc_final: 0.7230 (mt) outliers start: 19 outliers final: 9 residues processed: 59 average time/residue: 0.1098 time to fit residues: 8.6740 Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131707 restraints weight = 3525.931| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.69 r_work: 0.3395 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3199 Z= 0.243 Angle : 0.591 9.992 4372 Z= 0.304 Chirality : 0.042 0.201 505 Planarity : 0.004 0.035 524 Dihedral : 4.268 20.121 423 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 6.01 % Allowed : 20.42 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.43), residues: 383 helix: 1.21 (0.29), residues: 323 sheet: None (None), residues: 0 loop : 0.22 (0.88), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 71 TYR 0.015 0.001 TYR A 298 ARG 0.002 0.000 ARG A 277 *********************** 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 62 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6929 (pt0) REVERT: A 146 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8492 (t) REVERT: A 265 TRP cc_start: 0.8379 (t60) cc_final: 0.8101 (t60) REVERT: A 280 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.6555 (m-80) REVERT: A 340 ASN cc_start: 0.8305 (p0) cc_final: 0.7298 (t0) REVERT: A 385 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8288 (tp) outliers start: 20 outliers final: 12 residues processed: 56 average time/residue: 0.1076 time to fit residues: 8.0915 Evaluate side-chains 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN 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 = 0.152249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131532 restraints weight = 3570.243| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.70 r_work: 0.3402 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3199 Z= 0.237 Angle : 0.587 9.865 4372 Z= 0.301 Chirality : 0.042 0.207 505 Planarity : 0.004 0.036 524 Dihedral : 4.254 20.157 423 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.41 % Allowed : 19.82 % Favored : 74.77 % 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: 1.63 (0.43), residues: 383 helix: 1.34 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.07 (0.85), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 71 TYR 0.014 0.001 TYR A 298 ARG 0.001 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6912 (pt0) REVERT: A 146 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8500 (t) REVERT: A 265 TRP cc_start: 0.8431 (t60) cc_final: 0.8187 (t60) REVERT: A 280 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.6563 (m-80) REVERT: A 340 ASN cc_start: 0.8377 (p0) cc_final: 0.7283 (t0) REVERT: A 385 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8278 (tp) outliers start: 18 outliers final: 11 residues processed: 54 average time/residue: 0.1271 time to fit residues: 9.0414 Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131851 restraints weight = 3482.385| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.65 r_work: 0.3406 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3199 Z= 0.236 Angle : 0.594 9.959 4372 Z= 0.303 Chirality : 0.042 0.214 505 Planarity : 0.004 0.036 524 Dihedral : 4.265 20.348 423 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.80 % Allowed : 21.02 % 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: 1.66 (0.43), residues: 383 helix: 1.35 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.13 (0.85), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 71 TYR 0.011 0.001 TYR A 445 ARG 0.001 0.000 ARG A 138 *********************** 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: 16 poor density : 44 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7052 (pt0) REVERT: A 265 TRP cc_start: 0.8451 (t60) cc_final: 0.8204 (t60) REVERT: A 280 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.6577 (m-80) REVERT: A 340 ASN cc_start: 0.8286 (p0) cc_final: 0.7241 (t0) REVERT: A 385 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8261 (tp) outliers start: 16 outliers final: 11 residues processed: 53 average time/residue: 0.1064 time to fit residues: 7.5790 Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.3325 > 50: distance: 17 - 22: 29.046 distance: 18 - 47: 23.421 distance: 22 - 23: 37.321 distance: 23 - 24: 42.390 distance: 23 - 26: 46.737 distance: 24 - 25: 33.332 distance: 24 - 29: 14.566 distance: 26 - 27: 56.645 distance: 26 - 28: 23.223 distance: 29 - 30: 16.436 distance: 30 - 31: 39.419 distance: 30 - 33: 52.062 distance: 31 - 32: 35.716 distance: 31 - 40: 39.504 distance: 33 - 34: 42.082 distance: 34 - 35: 9.651 distance: 34 - 36: 23.118 distance: 35 - 37: 33.366 distance: 36 - 38: 39.682 distance: 37 - 39: 33.582 distance: 38 - 39: 41.242 distance: 40 - 41: 40.242 distance: 41 - 42: 25.617 distance: 41 - 44: 35.603 distance: 42 - 43: 19.418 distance: 42 - 47: 33.078 distance: 44 - 45: 48.654 distance: 44 - 46: 40.469 distance: 47 - 48: 16.649 distance: 48 - 49: 19.385 distance: 48 - 51: 42.817 distance: 49 - 50: 48.387 distance: 49 - 55: 56.753 distance: 51 - 52: 19.970 distance: 52 - 53: 38.473 distance: 52 - 54: 52.513 distance: 55 - 56: 11.018 distance: 56 - 57: 45.841 distance: 56 - 59: 38.611 distance: 57 - 58: 50.344 distance: 57 - 62: 40.461 distance: 59 - 60: 43.125 distance: 59 - 61: 5.419 distance: 62 - 63: 62.249 distance: 63 - 64: 53.085 distance: 63 - 66: 52.463 distance: 64 - 65: 7.886 distance: 64 - 70: 65.653 distance: 66 - 67: 12.411 distance: 67 - 68: 18.849 distance: 67 - 69: 29.372 distance: 70 - 71: 38.738 distance: 71 - 72: 23.475 distance: 71 - 74: 49.785 distance: 72 - 73: 16.660 distance: 72 - 82: 51.815 distance: 74 - 75: 39.335 distance: 75 - 76: 46.764 distance: 75 - 77: 39.153 distance: 76 - 78: 27.515 distance: 77 - 79: 41.290 distance: 78 - 80: 38.638 distance: 79 - 80: 39.426 distance: 80 - 81: 41.254 distance: 82 - 83: 56.712 distance: 83 - 84: 23.543 distance: 83 - 86: 33.199 distance: 84 - 85: 53.104 distance: 84 - 89: 36.970 distance: 86 - 87: 40.788 distance: 89 - 90: 24.682 distance: 90 - 91: 39.039 distance: 90 - 93: 45.616 distance: 91 - 92: 39.064 distance: 91 - 100: 39.676 distance: 93 - 94: 45.026 distance: 94 - 95: 30.874 distance: 95 - 96: 38.767 distance: 96 - 97: 23.217 distance: 97 - 98: 28.009 distance: 97 - 99: 17.653 distance: 100 - 101: 56.664 distance: 101 - 102: 3.924 distance: 101 - 104: 9.845 distance: 102 - 112: 34.179 distance: 104 - 105: 31.110 distance: 105 - 106: 44.479 distance: 105 - 107: 8.290 distance: 106 - 108: 40.069 distance: 107 - 109: 40.758 distance: 108 - 110: 10.458 distance: 109 - 110: 25.722 distance: 110 - 111: 7.631