Starting phenix.real_space_refine on Sun Aug 4 07:49:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/08_2024/8fgx_29077_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/08_2024/8fgx_29077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/08_2024/8fgx_29077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/08_2024/8fgx_29077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/08_2024/8fgx_29077_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/08_2024/8fgx_29077_trim.cif" } resolution = 2.62 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= 0.000 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: 5 Type Number sf(0) Gaussians S 22 5.16 5 C 3186 2.51 5 N 838 2.21 5 O 980 1.98 5 H 4873 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9899 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3252 Classifications: {'peptide': 213} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "B" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3190 Classifications: {'peptide': 216} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 202} Chain breaks: 1 Chain: "C" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3415 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain breaks: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.59, per 1000 atoms: 0.56 Number of scatterers: 9899 At special positions: 0 Unit cell: (106.683, 99.24, 83.527, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 980 8.00 N 838 7.00 C 3186 6.00 H 4873 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 419 " - pdb=" SG CYS C 435 " distance=2.03 Simple disulfide: pdb=" SG CYS C 517 " - pdb=" SG CYS C 584 " distance=2.03 Simple disulfide: pdb=" SG CYS C 548 " - pdb=" SG CYS C 563 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 C 701 " - " ASN C 396 " " NAG C 702 " - " ASN C 453 " " NAG C 703 " - " ASN C 494 " Time building additional restraints: 7.23 Conformation dependent library (CDL) restraints added in 980.6 milliseconds 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 13 sheets defined 11.3% alpha, 46.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.701A pdb=" N PHE A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.686A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.727A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'C' and resid 432 through 437 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 506 through 511 removed outlier: 3.812A pdb=" N THR C 510 " --> pdb=" O LYS C 507 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER C 511 " --> pdb=" O GLY C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 550 removed outlier: 4.006A pdb=" N LYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 626 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU A 11 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 33 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR A 49 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU A 11 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 97 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 118 removed outlier: 4.963A pdb=" N SER A 131 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU A 181 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL A 133 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 179 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU A 135 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A 177 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASN A 137 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 175 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.415A pdb=" N MET B 34 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.684A pdb=" N CYS B 96 " --> pdb=" O TRP B 111 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP B 111 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY B 98 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.061A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.061A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.313A pdb=" N TYR B 202 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 405 through 410 removed outlier: 6.903A pdb=" N VAL C 410 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N HIS C 417 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 486 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE C 469 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS C 488 " --> pdb=" O LYS C 467 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE C 466 " --> pdb=" O TRP C 445 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TRP C 445 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 536 through 539 removed outlier: 3.727A pdb=" N THR C 520 " --> pdb=" O PRO C 581 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU C 582 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N CYS C 563 " --> pdb=" O VAL C 543 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 486 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: 3.86 Time building geometry restraints manager: 7.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4858 1.03 - 1.23: 18 1.23 - 1.42: 2174 1.42 - 1.61: 2942 1.61 - 1.81: 29 Bond restraints: 10021 Sorted by residual: bond pdb=" N ILE C 391 " pdb=" CA ILE C 391 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.58e+00 bond pdb=" N ILE C 391 " pdb=" H ILE C 391 " ideal model delta sigma weight residual 0.860 0.888 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C1 NAG C 702 " pdb=" O5 NAG C 702 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" C1 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" C1 NAG C 703 " pdb=" O5 NAG C 703 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.37e+00 ... (remaining 10016 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.71: 173 106.71 - 113.53: 11866 113.53 - 120.35: 2912 120.35 - 127.17: 3013 127.17 - 133.99: 79 Bond angle restraints: 18043 Sorted by residual: angle pdb=" CA PRO C 608 " pdb=" C PRO C 608 " pdb=" N GLY C 609 " ideal model delta sigma weight residual 114.66 116.82 -2.16 1.34e+00 5.57e-01 2.60e+00 angle pdb=" CA ILE C 391 " pdb=" N ILE C 391 " pdb=" H ILE C 391 " ideal model delta sigma weight residual 114.00 109.40 4.60 3.00e+00 1.11e-01 2.35e+00 angle pdb=" N ALA A 51 " pdb=" CA ALA A 51 " pdb=" C ALA A 51 " ideal model delta sigma weight residual 110.80 114.05 -3.25 2.13e+00 2.20e-01 2.33e+00 angle pdb=" N SER C 597 " pdb=" CA SER C 597 " pdb=" C SER C 597 " ideal model delta sigma weight residual 113.18 111.31 1.87 1.33e+00 5.65e-01 1.98e+00 angle pdb=" C TYR A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta sigma weight residual 121.54 124.17 -2.63 1.91e+00 2.74e-01 1.90e+00 ... (remaining 18038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 4525 17.41 - 34.81: 173 34.81 - 52.22: 88 52.22 - 69.62: 40 69.62 - 87.03: 15 Dihedral angle restraints: 4841 sinusoidal: 2631 harmonic: 2210 Sorted by residual: dihedral pdb=" CA ARG A 142 " pdb=" C ARG A 142 " pdb=" N GLU A 143 " pdb=" CA GLU A 143 " ideal model delta harmonic sigma weight residual -180.00 -162.97 -17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA PHE B 95 " pdb=" C PHE B 95 " pdb=" N CYS B 96 " pdb=" CA CYS B 96 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 68.07 24.93 1 1.00e+01 1.00e-02 8.94e+00 ... (remaining 4838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 504 0.033 - 0.065: 187 0.065 - 0.097: 37 0.097 - 0.130: 58 0.130 - 0.162: 2 Chirality restraints: 788 Sorted by residual: chirality pdb=" C1 NAG C 703 " pdb=" ND2 ASN C 494 " pdb=" C2 NAG C 703 " pdb=" O5 NAG C 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA ILE C 531 " pdb=" N ILE C 531 " pdb=" C ILE C 531 " pdb=" CB ILE C 531 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE A 21 " pdb=" N ILE A 21 " pdb=" C ILE A 21 " pdb=" CB ILE A 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 785 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 607 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO C 608 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 608 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 608 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 156 " -0.022 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 157 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 209 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO B 210 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.014 5.00e-02 4.00e+02 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 849 2.22 - 2.82: 21627 2.82 - 3.41: 25899 3.41 - 4.01: 38020 4.01 - 4.60: 56223 Nonbonded interactions: 142618 Sorted by model distance: nonbonded pdb=" OE1 GLU A 123 " pdb=" H GLU A 123 " model vdw 1.630 2.450 nonbonded pdb=" HH TYR A 36 " pdb=" OE1 GLN A 89 " model vdw 1.633 2.450 nonbonded pdb=" O ASP A 82 " pdb=" HH TYR A 86 " model vdw 1.648 2.450 nonbonded pdb="HE22 GLN B 6 " pdb=" O TYR B 94 " model vdw 1.665 2.450 nonbonded pdb=" OE1 GLN C 409 " pdb="HE21 GLN C 415 " model vdw 1.671 2.450 ... (remaining 142613 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 8.510 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 36.250 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5148 Z= 0.184 Angle : 0.446 4.136 7002 Z= 0.230 Chirality : 0.044 0.162 788 Planarity : 0.003 0.041 883 Dihedral : 9.989 87.028 1879 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.41 (0.36), residues: 631 helix: -0.33 (0.92), residues: 33 sheet: 0.66 (0.31), residues: 270 loop : 1.58 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.002 0.001 HIS A 198 PHE 0.010 0.001 PHE A 46 TYR 0.006 0.001 TYR A 91 ARG 0.002 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 3.3390 time to fit residues: 200.1854 Evaluate side-chains 42 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.0370 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5148 Z= 0.229 Angle : 0.509 4.432 7002 Z= 0.274 Chirality : 0.045 0.154 788 Planarity : 0.004 0.036 883 Dihedral : 5.245 41.739 745 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.18 % Allowed : 6.29 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.26 (0.35), residues: 631 helix: -0.27 (0.81), residues: 33 sheet: 0.61 (0.30), residues: 277 loop : 1.43 (0.39), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 428 HIS 0.004 0.001 HIS C 434 PHE 0.013 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.005 0.001 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8517 (tt0) cc_final: 0.8200 (tt0) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 3.0265 time to fit residues: 135.4061 Evaluate side-chains 39 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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: 0.8902 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5148 Z= 0.323 Angle : 0.510 4.345 7002 Z= 0.272 Chirality : 0.045 0.148 788 Planarity : 0.004 0.035 883 Dihedral : 4.878 34.396 745 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.18 % Allowed : 6.83 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.17 (0.34), residues: 631 helix: -0.18 (0.81), residues: 34 sheet: 0.60 (0.29), residues: 278 loop : 1.29 (0.39), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.002 0.001 HIS C 417 PHE 0.013 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.003 0.001 ARG C 416 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8521 (tt0) cc_final: 0.8249 (tt0) REVERT: C 619 ASP cc_start: 0.8485 (p0) cc_final: 0.8243 (p0) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 2.7025 time to fit residues: 112.9228 Evaluate side-chains 37 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8889 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5148 Z= 0.226 Angle : 0.493 4.284 7002 Z= 0.261 Chirality : 0.045 0.149 788 Planarity : 0.003 0.036 883 Dihedral : 4.538 28.637 745 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.12 (0.34), residues: 631 helix: -0.23 (0.82), residues: 34 sheet: 0.60 (0.29), residues: 274 loop : 1.22 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.002 0.001 HIS C 434 PHE 0.011 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.003 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 619 ASP cc_start: 0.8479 (p0) cc_final: 0.8241 (p0) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 2.7284 time to fit residues: 119.7722 Evaluate side-chains 39 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 0.0570 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 54 optimal weight: 0.0770 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5148 Z= 0.166 Angle : 0.486 4.896 7002 Z= 0.256 Chirality : 0.045 0.152 788 Planarity : 0.003 0.036 883 Dihedral : 4.299 26.720 745 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.18 % Allowed : 7.55 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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 (0.34), residues: 631 helix: -0.22 (0.83), residues: 34 sheet: 0.74 (0.30), residues: 273 loop : 1.19 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 PHE 0.009 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.004 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8467 (tt0) cc_final: 0.8140 (tt0) REVERT: C 619 ASP cc_start: 0.8523 (p0) cc_final: 0.8273 (p0) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 2.8248 time to fit residues: 126.7160 Evaluate side-chains 38 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.0370 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5148 Z= 0.328 Angle : 0.521 5.134 7002 Z= 0.275 Chirality : 0.045 0.150 788 Planarity : 0.003 0.039 883 Dihedral : 4.323 24.503 745 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.36 % Allowed : 7.73 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.11 (0.34), residues: 631 helix: -0.07 (0.83), residues: 34 sheet: 0.64 (0.30), residues: 274 loop : 1.14 (0.37), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 PHE 0.013 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.010 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8468 (tt0) cc_final: 0.8165 (tt0) REVERT: C 554 ASP cc_start: 0.8491 (m-30) cc_final: 0.8027 (p0) REVERT: C 619 ASP cc_start: 0.8584 (p0) cc_final: 0.8338 (p0) outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 2.8403 time to fit residues: 130.5159 Evaluate side-chains 38 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.8896 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5148 Z= 0.231 Angle : 0.511 5.725 7002 Z= 0.269 Chirality : 0.044 0.152 788 Planarity : 0.003 0.039 883 Dihedral : 4.217 23.161 745 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.14 (0.34), residues: 631 helix: -0.12 (0.84), residues: 35 sheet: 0.69 (0.30), residues: 272 loop : 1.14 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 PHE 0.011 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.006 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8475 (tt0) cc_final: 0.8183 (tt0) REVERT: C 554 ASP cc_start: 0.8485 (m-30) cc_final: 0.8051 (p0) REVERT: C 555 TYR cc_start: 0.6753 (m-80) cc_final: 0.5538 (m-80) REVERT: C 619 ASP cc_start: 0.8598 (p0) cc_final: 0.8368 (p0) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 2.5865 time to fit residues: 100.3364 Evaluate side-chains 36 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.8911 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5148 Z= 0.289 Angle : 0.529 6.148 7002 Z= 0.278 Chirality : 0.044 0.150 788 Planarity : 0.003 0.040 883 Dihedral : 4.193 21.379 745 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.13 (0.34), residues: 631 helix: -0.09 (0.88), residues: 35 sheet: 0.68 (0.30), residues: 272 loop : 1.13 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.003 0.001 HIS A 53 PHE 0.012 0.001 PHE B 95 TYR 0.006 0.001 TYR A 49 ARG 0.006 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8474 (tt0) cc_final: 0.8193 (tt0) REVERT: C 554 ASP cc_start: 0.8456 (m-30) cc_final: 0.8019 (p0) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 2.6474 time to fit residues: 110.7635 Evaluate side-chains 37 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 62.0547 > 50: distance: 140 - 149: 28.033 distance: 149 - 150: 28.888 distance: 149 - 158: 43.900 distance: 150 - 151: 38.760 distance: 150 - 153: 34.268 distance: 150 - 159: 32.150 distance: 151 - 152: 6.996 distance: 151 - 171: 33.816 distance: 153 - 154: 41.215 distance: 153 - 160: 24.419 distance: 153 - 161: 31.923 distance: 154 - 155: 20.663 distance: 154 - 162: 15.541 distance: 154 - 163: 23.067 distance: 155 - 156: 9.903 distance: 155 - 164: 4.588 distance: 155 - 165: 9.188 distance: 156 - 157: 3.909 distance: 156 - 166: 4.477 distance: 156 - 167: 3.356 distance: 171 - 172: 13.071 distance: 171 - 177: 12.289 distance: 172 - 173: 21.611 distance: 172 - 175: 13.680 distance: 172 - 178: 9.618 distance: 173 - 174: 4.884 distance: 173 - 185: 46.611 distance: 175 - 176: 4.495 distance: 175 - 179: 7.995 distance: 175 - 180: 16.514 distance: 176 - 177: 9.903 distance: 176 - 181: 7.551 distance: 176 - 182: 5.516 distance: 177 - 183: 10.888 distance: 177 - 184: 33.662 distance: 185 - 186: 23.858 distance: 185 - 193: 11.324 distance: 186 - 187: 25.720 distance: 186 - 189: 12.275 distance: 186 - 194: 27.400 distance: 187 - 204: 47.645 distance: 189 - 190: 21.696 distance: 189 - 191: 17.231 distance: 189 - 195: 23.159 distance: 190 - 192: 15.951 distance: 190 - 196: 12.262 distance: 190 - 197: 13.232 distance: 191 - 198: 7.029 distance: 191 - 199: 6.990 distance: 191 - 200: 5.691 distance: 192 - 201: 5.115 distance: 192 - 202: 8.682 distance: 192 - 203: 7.656 distance: 204 - 205: 9.380 distance: 204 - 210: 12.750 distance: 205 - 206: 35.028 distance: 205 - 208: 7.853 distance: 205 - 211: 29.943 distance: 206 - 207: 29.912 distance: 206 - 215: 12.841 distance: 208 - 209: 14.000 distance: 208 - 212: 41.254 distance: 208 - 213: 17.440 distance: 209 - 214: 15.105 distance: 215 - 216: 11.972 distance: 215 - 223: 18.231 distance: 216 - 217: 20.044 distance: 216 - 219: 9.077 distance: 216 - 224: 19.281 distance: 217 - 218: 15.434 distance: 217 - 234: 7.143 distance: 219 - 220: 14.609 distance: 219 - 225: 39.566 distance: 219 - 226: 25.603 distance: 220 - 221: 16.760 distance: 220 - 222: 7.735 distance: 220 - 227: 6.331 distance: 221 - 228: 5.875 distance: 221 - 229: 7.678 distance: 221 - 230: 9.787 distance: 222 - 231: 4.824 distance: 222 - 233: 3.821 distance: 234 - 235: 12.112 distance: 234 - 240: 10.367 distance: 235 - 236: 22.869 distance: 235 - 238: 7.168 distance: 235 - 241: 8.008 distance: 236 - 237: 17.228 distance: 236 - 248: 32.307 distance: 238 - 239: 8.838 distance: 238 - 242: 17.329 distance: 238 - 243: 13.431 distance: 239 - 240: 8.850 distance: 239 - 244: 12.262 distance: 239 - 245: 3.303 distance: 240 - 246: 7.893 distance: 240 - 247: 9.868 distance: 248 - 249: 16.112 distance: 248 - 254: 16.464 distance: 249 - 250: 22.841 distance: 249 - 252: 11.993 distance: 249 - 255: 26.376 distance: 250 - 251: 10.631 distance: 250 - 259: 40.894 distance: 251 - 288: 38.543 distance: 252 - 253: 14.569 distance: 252 - 256: 16.802 distance: 252 - 257: 16.944 distance: 253 - 258: 24.343 distance: 259 - 260: 16.065 distance: 259 - 268: 10.578 distance: 260 - 261: 28.485 distance: 260 - 263: 12.654 distance: 260 - 269: 12.940 distance: 261 - 262: 16.591 distance: 261 - 281: 9.328 distance: 263 - 264: 10.392 distance: 263 - 270: 9.330 distance: 263 - 271: 9.055 distance: 264 - 265: 3.357 distance: 264 - 272: 11.296 distance: 264 - 273: 10.445 distance: 265 - 266: 9.788 distance: 265 - 274: 5.286 distance: 265 - 275: 3.441 distance: 266 - 267: 4.908 distance: 266 - 277: 3.519 distance: 281 - 282: 23.523 distance: 282 - 283: 33.874 distance: 282 - 286: 38.629 distance: 282 - 287: 35.026 distance: 283 - 284: 8.544 distance: 283 - 288: 14.933 distance: 288 - 289: 12.970 distance: 288 - 296: 24.256 distance: 289 - 290: 15.939 distance: 289 - 292: 30.045 distance: 289 - 297: 34.861 distance: 290 - 291: 10.864 distance: 290 - 300: 19.740 distance: 292 - 293: 9.633 distance: 292 - 298: 21.750 distance: 292 - 299: 9.204 distance: 293 - 294: 10.184 distance: 293 - 295: 14.431