Starting phenix.real_space_refine on Mon Sep 23 17:46:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2e_38852/09_2024/8y2e_38852.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2e_38852/09_2024/8y2e_38852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2e_38852/09_2024/8y2e_38852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2e_38852/09_2024/8y2e_38852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2e_38852/09_2024/8y2e_38852.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2e_38852/09_2024/8y2e_38852.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 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 23 5.16 5 C 2813 2.51 5 N 659 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4214 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4163 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 504} Chain breaks: 2 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'CXQ': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.90, per 1000 atoms: 0.69 Number of scatterers: 4214 At special positions: 0 Unit cell: (74.8, 69.7, 91.8, 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 23 16.00 O 719 8.00 N 659 7.00 C 2813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 189 " distance=2.04 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 181 " " NAG A 702 " - " ASN A 188 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 366.5 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 79.4% alpha, 0.4% 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 66 through 78 removed outlier: 3.780A pdb=" N PHE A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.782A pdb=" N TYR A 88 " --> pdb=" O TRP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.598A pdb=" N ILE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 140 through 170 removed outlier: 3.610A pdb=" N VAL A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 237 through 255 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.874A pdb=" N GLY A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.830A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 306' Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.523A pdb=" N CYS A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.874A pdb=" N ALA A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 376 Processing helix chain 'A' and resid 378 through 382 removed outlier: 3.685A pdb=" N VAL A 382 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.521A pdb=" N TRP A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 461 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 467 through 479 removed outlier: 4.111A pdb=" N VAL A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 498 Processing helix chain 'A' and resid 500 through 513 Processing helix chain 'A' and resid 517 through 526 Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.506A pdb=" N PHE A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 570 removed outlier: 3.544A pdb=" N ASN A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 583 removed outlier: 4.293A pdb=" N ILE A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 575 " --> pdb=" O MET A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 removed outlier: 3.593A pdb=" N TYR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 609 through 612 Processing helix chain 'A' and resid 613 through 618 removed outlier: 3.898A pdb=" N TRP A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 547 through 548 268 hydrogen bonds defined for protein. 789 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: 0.80 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1101 1.34 - 1.46: 925 1.46 - 1.58: 2282 1.58 - 1.70: 3 1.70 - 1.82: 34 Bond restraints: 4345 Sorted by residual: bond pdb=" C1 CXQ A 703 " pdb=" C5 CXQ A 703 " ideal model delta sigma weight residual 1.519 1.633 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C1 CXQ A 703 " pdb=" C4 CXQ A 703 " ideal model delta sigma weight residual 1.513 1.594 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C17 CXQ A 703 " pdb=" N1 CXQ A 703 " ideal model delta sigma weight residual 1.448 1.510 -0.062 2.00e-02 2.50e+03 9.70e+00 bond pdb=" C1 CXQ A 703 " pdb=" O1 CXQ A 703 " ideal model delta sigma weight residual 1.397 1.458 -0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" N ILE A 268 " pdb=" CA ILE A 268 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.49e+00 ... (remaining 4340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 5799 1.86 - 3.71: 114 3.71 - 5.57: 15 5.57 - 7.43: 2 7.43 - 9.28: 1 Bond angle restraints: 5931 Sorted by residual: angle pdb=" CA PRO A 584 " pdb=" N PRO A 584 " pdb=" CD PRO A 584 " ideal model delta sigma weight residual 112.00 106.62 5.38 1.40e+00 5.10e-01 1.48e+01 angle pdb=" CA ASP A 191 " pdb=" C ASP A 191 " pdb=" O ASP A 191 " ideal model delta sigma weight residual 120.92 117.41 3.51 1.04e+00 9.25e-01 1.14e+01 angle pdb=" CA PHE A 531 " pdb=" CB PHE A 531 " pdb=" CG PHE A 531 " ideal model delta sigma weight residual 113.80 117.14 -3.34 1.00e+00 1.00e+00 1.12e+01 angle pdb=" CA ARG A 606 " pdb=" CB ARG A 606 " pdb=" CG ARG A 606 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA LEU A 250 " pdb=" CB LEU A 250 " pdb=" CG LEU A 250 " ideal model delta sigma weight residual 116.30 125.58 -9.28 3.50e+00 8.16e-02 7.04e+00 ... (remaining 5926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 2330 28.42 - 56.85: 151 56.85 - 85.27: 11 85.27 - 113.70: 0 113.70 - 142.12: 2 Dihedral angle restraints: 2494 sinusoidal: 973 harmonic: 1521 Sorted by residual: dihedral pdb=" C1 CXQ A 703 " pdb=" C6 CXQ A 703 " pdb=" O1 CXQ A 703 " pdb=" C8 CXQ A 703 " ideal model delta sinusoidal sigma weight residual 158.12 16.00 142.12 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C1 CXQ A 703 " pdb=" C6 CXQ A 703 " pdb=" O1 CXQ A 703 " pdb=" C7 CXQ A 703 " ideal model delta sinusoidal sigma weight residual 280.48 139.54 140.94 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CA TRP A 132 " pdb=" C TRP A 132 " pdb=" N LYS A 133 " pdb=" CA LYS A 133 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 529 0.046 - 0.093: 116 0.093 - 0.139: 30 0.139 - 0.185: 2 0.185 - 0.231: 1 Chirality restraints: 678 Sorted by residual: chirality pdb=" CA ILE A 268 " pdb=" N ILE A 268 " pdb=" C ILE A 268 " pdb=" CB ILE A 268 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C2 CXQ A 703 " pdb=" C13 CXQ A 703 " pdb=" C7 CXQ A 703 " pdb=" N1 CXQ A 703 " both_signs ideal model delta sigma weight residual False 2.74 2.92 -0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA PRO A 584 " pdb=" N PRO A 584 " pdb=" C PRO A 584 " pdb=" CB PRO A 584 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 675 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 394 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.54e+00 pdb=" N PRO A 395 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 395 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 395 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 189 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C CYS A 189 " 0.035 2.00e-02 2.50e+03 pdb=" O CYS A 189 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 190 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.016 2.00e-02 2.50e+03 1.47e-02 2.71e+00 pdb=" CG ASN A 181 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.013 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.015 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1154 2.81 - 3.33: 3834 3.33 - 3.85: 6643 3.85 - 4.38: 7416 4.38 - 4.90: 13745 Nonbonded interactions: 32792 Sorted by model distance: nonbonded pdb=" NH1 ARG A 237 " pdb=" OD1 ASN A 466 " model vdw 2.283 3.120 nonbonded pdb=" O ARG A 237 " pdb=" OG1 THR A 241 " model vdw 2.312 3.040 nonbonded pdb=" OG SER A 186 " pdb=" OE2 GLU A 215 " model vdw 2.340 3.040 nonbonded pdb=" N ASP A 79 " pdb=" OD1 ASP A 79 " model vdw 2.409 3.120 nonbonded pdb=" O PHE A 498 " pdb=" NE2 GLN A 611 " model vdw 2.419 3.120 ... (remaining 32787 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.990 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:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.005 0.114 4345 Z= 0.299 Angle : 0.610 9.283 5931 Z= 0.317 Chirality : 0.041 0.231 678 Planarity : 0.005 0.059 723 Dihedral : 17.534 142.121 1519 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 23.76 % Favored : 76.24 % 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: 1.57 (0.38), residues: 522 helix: 1.92 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -1.00 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 132 HIS 0.002 0.001 HIS A 225 PHE 0.016 0.001 PHE A 451 TYR 0.010 0.001 TYR A 575 ARG 0.001 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.435 Fit side-chains REVERT: A 126 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7415 (mt-10) REVERT: A 531 PHE cc_start: 0.8123 (t80) cc_final: 0.7252 (t80) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1648 time to fit residues: 10.2987 Evaluate side-chains 44 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.0070 chunk 14 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4345 Z= 0.192 Angle : 0.533 7.487 5931 Z= 0.268 Chirality : 0.037 0.122 678 Planarity : 0.004 0.060 723 Dihedral : 8.790 116.403 636 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.71 % Allowed : 22.85 % Favored : 74.43 % 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: 1.89 (0.39), residues: 522 helix: 2.18 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -0.97 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 PHE 0.012 0.001 PHE A 412 TYR 0.013 0.001 TYR A 548 ARG 0.002 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.448 Fit side-chains REVERT: A 320 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.6434 (t80) REVERT: A 424 MET cc_start: 0.6724 (mtp) cc_final: 0.6344 (mtt) REVERT: A 514 GLN cc_start: 0.7052 (tp40) cc_final: 0.6534 (pt0) outliers start: 12 outliers final: 8 residues processed: 57 average time/residue: 0.1415 time to fit residues: 10.6779 Evaluate side-chains 54 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 517 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4345 Z= 0.188 Angle : 0.503 6.342 5931 Z= 0.253 Chirality : 0.037 0.116 678 Planarity : 0.004 0.060 723 Dihedral : 7.946 106.282 636 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.85 % Allowed : 21.72 % Favored : 74.43 % 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: 1.83 (0.38), residues: 522 helix: 2.12 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.13 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 477 PHE 0.014 0.001 PHE A 451 TYR 0.009 0.001 TYR A 575 ARG 0.001 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 44 time to evaluate : 0.472 Fit side-chains REVERT: A 126 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7579 (mt-10) REVERT: A 320 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.6295 (t80) REVERT: A 514 GLN cc_start: 0.7083 (tp40) cc_final: 0.6486 (pt0) outliers start: 17 outliers final: 13 residues processed: 57 average time/residue: 0.1502 time to fit residues: 11.3426 Evaluate side-chains 57 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4345 Z= 0.182 Angle : 0.494 6.037 5931 Z= 0.251 Chirality : 0.037 0.114 678 Planarity : 0.004 0.060 723 Dihedral : 7.298 95.786 636 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.75 % Allowed : 21.72 % Favored : 73.53 % 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: 1.80 (0.38), residues: 522 helix: 2.13 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.26 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 PHE 0.015 0.001 PHE A 451 TYR 0.009 0.001 TYR A 548 ARG 0.003 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 43 time to evaluate : 0.408 Fit side-chains REVERT: A 126 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7567 (mt-10) REVERT: A 156 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7945 (t80) REVERT: A 320 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.6336 (t80) REVERT: A 514 GLN cc_start: 0.7049 (tp40) cc_final: 0.6332 (pt0) outliers start: 21 outliers final: 15 residues processed: 59 average time/residue: 0.1371 time to fit residues: 10.7454 Evaluate side-chains 60 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4345 Z= 0.159 Angle : 0.472 6.292 5931 Z= 0.239 Chirality : 0.036 0.115 678 Planarity : 0.004 0.059 723 Dihedral : 6.979 89.868 636 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.98 % Allowed : 21.95 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.39), residues: 522 helix: 2.13 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -1.24 (0.52), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 556 HIS 0.002 0.001 HIS A 179 PHE 0.015 0.001 PHE A 451 TYR 0.008 0.001 TYR A 575 ARG 0.003 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 40 time to evaluate : 0.434 Fit side-chains REVERT: A 126 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7534 (mt-10) REVERT: A 156 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.7936 (t80) REVERT: A 320 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.6337 (t80) REVERT: A 416 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7901 (tp) REVERT: A 514 GLN cc_start: 0.7088 (tp40) cc_final: 0.6327 (pt0) outliers start: 22 outliers final: 13 residues processed: 59 average time/residue: 0.1293 time to fit residues: 10.3822 Evaluate side-chains 58 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4345 Z= 0.178 Angle : 0.488 6.417 5931 Z= 0.247 Chirality : 0.037 0.114 678 Planarity : 0.004 0.060 723 Dihedral : 6.815 86.568 636 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.20 % Allowed : 21.49 % Favored : 73.30 % 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: 1.80 (0.38), residues: 522 helix: 2.14 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.28 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 PHE 0.015 0.001 PHE A 451 TYR 0.010 0.001 TYR A 575 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 42 time to evaluate : 0.442 Fit side-chains REVERT: A 126 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7540 (mt-10) REVERT: A 156 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.7926 (t80) REVERT: A 320 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.6393 (t80) REVERT: A 416 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7910 (tp) REVERT: A 514 GLN cc_start: 0.7067 (tp40) cc_final: 0.6299 (pt0) outliers start: 23 outliers final: 18 residues processed: 61 average time/residue: 0.1392 time to fit residues: 11.2739 Evaluate side-chains 64 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 43 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4345 Z= 0.183 Angle : 0.496 6.959 5931 Z= 0.251 Chirality : 0.037 0.113 678 Planarity : 0.004 0.060 723 Dihedral : 6.719 84.401 636 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.75 % Allowed : 21.72 % Favored : 73.53 % 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: 1.77 (0.38), residues: 522 helix: 2.12 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.33 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 PHE 0.016 0.001 PHE A 451 TYR 0.012 0.001 TYR A 575 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 41 time to evaluate : 0.446 Fit side-chains REVERT: A 156 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.7942 (t80) REVERT: A 320 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.6323 (t80) REVERT: A 416 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7907 (tp) REVERT: A 514 GLN cc_start: 0.7071 (tp40) cc_final: 0.6290 (pt0) outliers start: 21 outliers final: 17 residues processed: 58 average time/residue: 0.1450 time to fit residues: 11.1728 Evaluate side-chains 61 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 41 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.0670 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 45 optimal weight: 0.0370 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4345 Z= 0.129 Angle : 0.446 6.116 5931 Z= 0.226 Chirality : 0.036 0.114 678 Planarity : 0.004 0.057 723 Dihedral : 6.412 79.527 636 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.07 % Allowed : 22.62 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.38), residues: 522 helix: 2.23 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.21 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 556 HIS 0.001 0.000 HIS A 179 PHE 0.016 0.001 PHE A 451 TYR 0.006 0.001 TYR A 575 ARG 0.001 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 41 time to evaluate : 0.438 Fit side-chains REVERT: A 126 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 156 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.7874 (t80) REVERT: A 320 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.6313 (t80) REVERT: A 416 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7865 (tp) outliers start: 18 outliers final: 13 residues processed: 57 average time/residue: 0.1470 time to fit residues: 11.0434 Evaluate side-chains 56 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4345 Z= 0.186 Angle : 0.494 6.963 5931 Z= 0.250 Chirality : 0.037 0.112 678 Planarity : 0.004 0.059 723 Dihedral : 6.420 79.146 636 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.85 % Allowed : 22.85 % Favored : 73.30 % 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: 1.86 (0.38), residues: 522 helix: 2.21 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.32 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 PHE 0.016 0.001 PHE A 451 TYR 0.010 0.001 TYR A 575 ARG 0.002 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 0.435 Fit side-chains REVERT: A 156 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.7915 (t80) REVERT: A 320 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.6324 (t80) REVERT: A 416 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7899 (tp) outliers start: 17 outliers final: 13 residues processed: 56 average time/residue: 0.1463 time to fit residues: 10.9256 Evaluate side-chains 57 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.7187 > 50: distance: 7 - 25: 6.515 distance: 19 - 25: 3.148 distance: 25 - 26: 5.867 distance: 26 - 27: 11.178 distance: 26 - 29: 9.824 distance: 27 - 28: 11.364 distance: 27 - 36: 12.714 distance: 29 - 30: 16.861 distance: 30 - 31: 12.266 distance: 31 - 32: 7.856 distance: 33 - 34: 4.673 distance: 33 - 35: 3.335 distance: 36 - 37: 9.546 distance: 37 - 38: 10.768 distance: 37 - 40: 8.162 distance: 38 - 39: 15.310 distance: 38 - 45: 10.088 distance: 40 - 41: 7.877 distance: 41 - 42: 4.966 distance: 45 - 46: 25.408 distance: 46 - 47: 24.108 distance: 47 - 48: 8.938 distance: 47 - 49: 15.287 distance: 49 - 50: 9.427 distance: 50 - 51: 15.157 distance: 50 - 53: 17.191 distance: 51 - 52: 3.812 distance: 51 - 54: 17.238 distance: 54 - 55: 23.071 distance: 55 - 56: 8.709 distance: 55 - 58: 10.472 distance: 56 - 57: 33.446 distance: 56 - 59: 8.921 distance: 59 - 60: 27.531 distance: 60 - 61: 28.359 distance: 61 - 62: 17.147 distance: 61 - 63: 22.810 distance: 63 - 64: 34.932 distance: 64 - 65: 22.402 distance: 64 - 67: 34.714 distance: 65 - 66: 32.434 distance: 65 - 70: 47.270 distance: 67 - 68: 39.238 distance: 67 - 69: 36.661 distance: 70 - 71: 30.748 distance: 71 - 72: 10.085 distance: 71 - 74: 18.107 distance: 72 - 73: 11.301 distance: 72 - 84: 20.920 distance: 74 - 75: 19.819 distance: 75 - 76: 18.128 distance: 75 - 77: 20.597 distance: 76 - 78: 12.619 distance: 77 - 79: 9.095 distance: 77 - 80: 11.395 distance: 78 - 79: 3.248 distance: 79 - 81: 9.969 distance: 80 - 82: 5.985 distance: 81 - 83: 7.922 distance: 82 - 83: 12.528 distance: 84 - 85: 15.729 distance: 85 - 86: 8.595 distance: 85 - 88: 10.798 distance: 86 - 87: 10.490 distance: 86 - 93: 5.599 distance: 88 - 89: 30.573 distance: 89 - 90: 16.670 distance: 90 - 91: 11.039 distance: 91 - 92: 3.846 distance: 93 - 94: 9.324 distance: 94 - 95: 11.415 distance: 94 - 97: 17.895 distance: 95 - 96: 6.006 distance: 95 - 101: 16.093 distance: 97 - 98: 20.478 distance: 97 - 99: 20.812 distance: 98 - 100: 9.757