Starting phenix.real_space_refine on Wed Mar 5 21:14:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cmh_45748/03_2025/9cmh_45748.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cmh_45748/03_2025/9cmh_45748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cmh_45748/03_2025/9cmh_45748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cmh_45748/03_2025/9cmh_45748.map" model { file = "/net/cci-nas-00/data/ceres_data/9cmh_45748/03_2025/9cmh_45748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cmh_45748/03_2025/9cmh_45748.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 18 5.16 5 C 2270 2.51 5 N 582 2.21 5 O 683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3553 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1324 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "B" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2229 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 7, 'TRANS': 278} Time building chain proxies: 3.06, per 1000 atoms: 0.86 Number of scatterers: 3553 At special positions: 0 Unit cell: (65.994, 51.76, 148.81, 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 18 16.00 O 683 8.00 N 582 7.00 C 2270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 64 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 439.9 milliseconds 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 850 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 31.5% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 5 through 27 Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.928A pdb=" N ALA A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 73' Processing helix chain 'A' and resid 77 through 104 removed outlier: 3.593A pdb=" N CYS A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 149 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 161 through 184 Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.624A pdb=" N ILE B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.788A pdb=" N ASN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 61 removed outlier: 6.313A pdb=" N VAL B 57 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA B 134 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B 59 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 61 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS B 138 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 195 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 83 removed outlier: 4.571A pdb=" N GLY B 153 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 155 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 139 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR B 135 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE B 161 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR B 133 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B 163 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS B 131 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS B 165 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 129 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER B 167 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR B 127 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS B 138 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'B' and resid 67 through 71 Processing sheet with id=AA6, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.575A pdb=" N LEU B 240 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE B 263 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 225 through 227 Processing sheet with id=AA8, first strand: chain 'B' and resid 249 through 254 removed outlier: 3.788A pdb=" N LEU B 291 " --> pdb=" O GLN B 249 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 468 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: 0.95 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1133 1.34 - 1.46: 688 1.46 - 1.58: 1771 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 3619 Sorted by residual: bond pdb=" CB VAL A 90 " pdb=" CG1 VAL A 90 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 bond pdb=" CG LEU A 130 " pdb=" CD2 LEU A 130 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.95e+00 bond pdb=" CB GLN A 156 " pdb=" CG GLN A 156 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CA MET A 22 " pdb=" CB MET A 22 " ideal model delta sigma weight residual 1.528 1.548 -0.019 1.56e-02 4.11e+03 1.55e+00 bond pdb=" CB MET A 62 " pdb=" CG MET A 62 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 ... (remaining 3614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 4856 2.89 - 5.78: 53 5.78 - 8.68: 8 8.68 - 11.57: 5 11.57 - 14.46: 1 Bond angle restraints: 4923 Sorted by residual: angle pdb=" CB MET A 22 " pdb=" CG MET A 22 " pdb=" SD MET A 22 " ideal model delta sigma weight residual 112.70 127.16 -14.46 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CA MET A 22 " pdb=" CB MET A 22 " pdb=" CG MET A 22 " ideal model delta sigma weight residual 114.10 122.94 -8.84 2.00e+00 2.50e-01 1.95e+01 angle pdb=" N MET A 22 " pdb=" CA MET A 22 " pdb=" CB MET A 22 " ideal model delta sigma weight residual 110.12 115.80 -5.68 1.47e+00 4.63e-01 1.50e+01 angle pdb=" CB MET A 62 " pdb=" CG MET A 62 " pdb=" SD MET A 62 " ideal model delta sigma weight residual 112.70 123.91 -11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA GLN A 156 " pdb=" CB GLN A 156 " pdb=" CG GLN A 156 " ideal model delta sigma weight residual 114.10 121.23 -7.13 2.00e+00 2.50e-01 1.27e+01 ... (remaining 4918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 1827 14.05 - 28.10: 203 28.10 - 42.15: 70 42.15 - 56.20: 13 56.20 - 70.25: 15 Dihedral angle restraints: 2128 sinusoidal: 793 harmonic: 1335 Sorted by residual: dihedral pdb=" CA MET A 131 " pdb=" C MET A 131 " pdb=" N VAL A 132 " pdb=" CA VAL A 132 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PRO A 28 " pdb=" C PRO A 28 " pdb=" N MET A 29 " pdb=" CA MET A 29 " ideal model delta harmonic sigma weight residual 180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA MET A 62 " pdb=" C MET A 62 " pdb=" N GLN A 63 " pdb=" CA GLN A 63 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 358 0.034 - 0.067: 145 0.067 - 0.100: 46 0.100 - 0.134: 22 0.134 - 0.167: 8 Chirality restraints: 579 Sorted by residual: chirality pdb=" CA MET A 22 " pdb=" N MET A 22 " pdb=" C MET A 22 " pdb=" CB MET A 22 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CB VAL B 118 " pdb=" CA VAL B 118 " pdb=" CG1 VAL B 118 " pdb=" CG2 VAL B 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CB VAL A 132 " pdb=" CA VAL A 132 " pdb=" CG1 VAL A 132 " pdb=" CG2 VAL A 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 576 not shown) Planarity restraints: 618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 75 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C GLN A 75 " 0.045 2.00e-02 2.50e+03 pdb=" O GLN A 75 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 76 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 81 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C VAL B 81 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL B 81 " 0.012 2.00e-02 2.50e+03 pdb=" N SER B 82 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 224 " 0.010 2.00e-02 2.50e+03 1.01e-02 2.04e+00 pdb=" CG TYR B 224 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 224 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 224 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 224 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 224 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 224 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 224 " 0.000 2.00e-02 2.50e+03 ... (remaining 615 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 71 2.65 - 3.22: 3684 3.22 - 3.78: 6189 3.78 - 4.34: 8430 4.34 - 4.90: 12976 Nonbonded interactions: 31350 Sorted by model distance: nonbonded pdb=" OG SER B 60 " pdb=" OH TYR B 129 " model vdw 2.092 3.040 nonbonded pdb=" O TYR B 232 " pdb=" OH TYR B 306 " model vdw 2.106 3.040 nonbonded pdb=" NE2 GLN B 140 " pdb=" OD1 ASP B 152 " model vdw 2.162 3.120 nonbonded pdb=" O ASP B 39 " pdb=" OH TYR B 264 " model vdw 2.163 3.040 nonbonded pdb=" OG1 THR B 135 " pdb=" O THR B 159 " model vdw 2.166 3.040 ... (remaining 31345 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.790 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3619 Z= 0.250 Angle : 0.873 14.461 4923 Z= 0.477 Chirality : 0.046 0.167 579 Planarity : 0.004 0.029 618 Dihedral : 14.789 70.254 1275 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.77 % Allowed : 24.81 % Favored : 74.42 % 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: -1.26 (0.39), residues: 462 helix: 1.65 (0.44), residues: 138 sheet: -2.12 (0.44), residues: 116 loop : -1.76 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 30 HIS 0.002 0.001 HIS B 241 PHE 0.014 0.002 PHE B 268 TYR 0.025 0.002 TYR B 224 ARG 0.003 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8544 (mm) cc_final: 0.8105 (pp) REVERT: A 48 GLU cc_start: 0.6256 (tt0) cc_final: 0.5640 (tt0) REVERT: A 144 ILE cc_start: 0.6878 (mm) cc_final: 0.6590 (tt) outliers start: 3 outliers final: 3 residues processed: 49 average time/residue: 0.2132 time to fit residues: 12.4719 Evaluate side-chains 43 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain B residue 247 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.0060 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.091054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.079569 restraints weight = 22224.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.081297 restraints weight = 13659.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.082360 restraints weight = 9687.200| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3619 Z= 0.181 Angle : 0.614 8.442 4923 Z= 0.321 Chirality : 0.043 0.134 579 Planarity : 0.004 0.051 618 Dihedral : 5.513 52.979 500 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.79 % Allowed : 20.46 % Favored : 77.75 % 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: -1.07 (0.40), residues: 462 helix: 2.06 (0.45), residues: 138 sheet: -2.05 (0.47), residues: 113 loop : -1.84 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 162 HIS 0.002 0.001 HIS A 141 PHE 0.012 0.001 PHE B 268 TYR 0.011 0.002 TYR B 130 ARG 0.003 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.4397 (ptt) cc_final: 0.3882 (ptt) REVERT: B 157 LYS cc_start: 0.8081 (tttt) cc_final: 0.7783 (ptmt) outliers start: 7 outliers final: 3 residues processed: 48 average time/residue: 0.1853 time to fit residues: 11.0806 Evaluate side-chains 40 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 296 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.087074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.075801 restraints weight = 22747.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.077403 restraints weight = 13935.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.078532 restraints weight = 9882.117| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3619 Z= 0.242 Angle : 0.655 8.806 4923 Z= 0.341 Chirality : 0.045 0.260 579 Planarity : 0.004 0.044 618 Dihedral : 4.795 17.749 496 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 25.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.84 % Allowed : 20.97 % Favored : 75.19 % 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: -1.13 (0.39), residues: 462 helix: 2.06 (0.44), residues: 133 sheet: -2.05 (0.48), residues: 108 loop : -1.87 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 162 HIS 0.004 0.001 HIS B 285 PHE 0.011 0.002 PHE B 104 TYR 0.009 0.002 TYR B 136 ARG 0.002 0.001 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9455 (tp) cc_final: 0.9221 (tp) REVERT: A 18 TRP cc_start: 0.6258 (t60) cc_final: 0.5873 (t60) REVERT: A 19 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8290 (pp) REVERT: A 31 ARG cc_start: 0.5871 (ttm170) cc_final: 0.4502 (ttm170) REVERT: A 48 GLU cc_start: 0.6816 (tt0) cc_final: 0.6366 (tt0) REVERT: A 118 MET cc_start: 0.4081 (ptt) cc_final: 0.3513 (ptt) REVERT: B 157 LYS cc_start: 0.8085 (tttt) cc_final: 0.7873 (ptmt) REVERT: B 315 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6882 (pp) outliers start: 15 outliers final: 6 residues processed: 48 average time/residue: 0.1720 time to fit residues: 10.1969 Evaluate side-chains 44 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.086761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.075565 restraints weight = 22727.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.077175 restraints weight = 14247.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.078203 restraints weight = 10165.767| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3619 Z= 0.225 Angle : 0.651 10.054 4923 Z= 0.333 Chirality : 0.044 0.271 579 Planarity : 0.004 0.035 618 Dihedral : 4.694 16.904 496 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.60 % Allowed : 20.97 % Favored : 74.42 % 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: -1.06 (0.39), residues: 462 helix: 2.18 (0.44), residues: 133 sheet: -1.84 (0.51), residues: 98 loop : -1.98 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 162 HIS 0.002 0.001 HIS B 285 PHE 0.012 0.001 PHE B 316 TYR 0.010 0.002 TYR B 133 ARG 0.003 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9435 (tp) cc_final: 0.9209 (tp) REVERT: A 18 TRP cc_start: 0.6196 (t60) cc_final: 0.5791 (t60) REVERT: A 19 LEU cc_start: 0.8835 (mm) cc_final: 0.8404 (pp) REVERT: A 52 MET cc_start: 0.8984 (ppp) cc_final: 0.8586 (ppp) REVERT: A 118 MET cc_start: 0.4155 (ptt) cc_final: 0.3523 (ptt) REVERT: B 244 ILE cc_start: 0.1685 (OUTLIER) cc_final: 0.1441 (mp) REVERT: B 291 LEU cc_start: 0.7902 (mt) cc_final: 0.7618 (mt) outliers start: 18 outliers final: 11 residues processed: 54 average time/residue: 0.1460 time to fit residues: 9.9934 Evaluate side-chains 50 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 299 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0921 > 50: distance: 33 - 63: 10.601 distance: 39 - 43: 3.476 distance: 40 - 71: 10.579 distance: 43 - 44: 7.423 distance: 44 - 45: 4.510 distance: 44 - 47: 7.449 distance: 45 - 46: 9.919 distance: 45 - 52: 23.273 distance: 46 - 80: 21.558 distance: 47 - 48: 4.250 distance: 48 - 49: 6.483 distance: 49 - 50: 15.717 distance: 49 - 51: 12.498 distance: 52 - 53: 15.121 distance: 53 - 54: 12.041 distance: 53 - 56: 4.732 distance: 54 - 55: 7.779 distance: 54 - 63: 11.915 distance: 55 - 85: 24.436 distance: 56 - 57: 4.078 distance: 57 - 58: 13.596 distance: 57 - 59: 9.546 distance: 58 - 60: 12.696 distance: 59 - 61: 15.349 distance: 60 - 62: 10.497 distance: 61 - 62: 10.393 distance: 63 - 64: 21.893 distance: 64 - 65: 23.942 distance: 64 - 67: 7.824 distance: 65 - 66: 19.599 distance: 65 - 71: 17.608 distance: 66 - 91: 27.972 distance: 67 - 68: 29.248 distance: 67 - 69: 11.621 distance: 68 - 70: 21.873 distance: 71 - 72: 17.329 distance: 72 - 73: 11.535 distance: 72 - 75: 15.226 distance: 73 - 74: 15.938 distance: 73 - 80: 9.462 distance: 74 - 98: 33.013 distance: 75 - 76: 23.591 distance: 76 - 77: 16.647 distance: 77 - 78: 14.926 distance: 77 - 79: 12.103 distance: 80 - 81: 21.518 distance: 81 - 82: 3.302 distance: 81 - 84: 11.871 distance: 82 - 85: 8.301 distance: 83 - 107: 27.985 distance: 85 - 86: 13.351 distance: 86 - 87: 17.527 distance: 86 - 89: 17.320 distance: 87 - 88: 8.769 distance: 87 - 91: 11.730 distance: 88 - 119: 41.599 distance: 89 - 90: 10.603 distance: 91 - 92: 19.855 distance: 92 - 93: 11.650 distance: 92 - 95: 24.957 distance: 93 - 94: 21.682 distance: 93 - 98: 42.751 distance: 94 - 123: 26.233 distance: 95 - 96: 14.429 distance: 95 - 97: 5.919 distance: 98 - 99: 11.098 distance: 99 - 100: 22.891 distance: 99 - 102: 37.357 distance: 100 - 101: 20.821 distance: 100 - 107: 4.350 distance: 102 - 103: 24.801 distance: 103 - 104: 8.890 distance: 104 - 105: 11.362 distance: 104 - 106: 6.776 distance: 108 - 109: 9.328 distance: 108 - 111: 11.895 distance: 109 - 110: 30.239 distance: 109 - 119: 10.043 distance: 111 - 112: 9.680 distance: 112 - 113: 7.023 distance: 112 - 114: 9.281 distance: 113 - 115: 12.004 distance: 114 - 116: 16.268 distance: 115 - 117: 11.728 distance: 116 - 117: 11.575 distance: 117 - 118: 11.814 distance: 119 - 120: 15.164 distance: 120 - 121: 25.498 distance: 121 - 122: 30.607 distance: 121 - 123: 16.291