Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vlm-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlm-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlm-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:07 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 299 and 0 Target number of residues in the AU: 299 Target solvent content: 0.6290 Checking the provided sequence file Detected sequence length: 219 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 438 Adjusted target solvent content: 0.46 Input MTZ file: 1vlm-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 18 Cell parameters: 65.648 70.734 93.922 90.000 90.000 90.000 Input sequence file: 1vlm-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3504 target number of atoms Had to go as low as 0.70 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 93.922 3.600 Wilson plot Bfac: 65.87 5411 reflections ( 99.69 % complete ) and 0 restraints for refining 3866 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3209 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2931 (Rfree = 0.000) for 3866 atoms. Found 24 (24 requested) and removed 45 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.58 Search for helices and strands: 0 residues in 0 chains, 3915 seeds are put forward NCS extension: 0 residues added, 3915 seeds are put forward Round 1: 149 peptides, 31 chains. Longest chain 12 peptides. Score 0.276 Round 2: 191 peptides, 32 chains. Longest chain 11 peptides. Score 0.422 Round 3: 205 peptides, 31 chains. Longest chain 13 peptides. Score 0.485 Round 4: 213 peptides, 32 chains. Longest chain 17 peptides. Score 0.497 Round 5: 234 peptides, 37 chains. Longest chain 14 peptides. Score 0.495 Taking the results from Round 4 Chains 32, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7411 restraints for refining 3176 atoms. 6719 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2459 (Rfree = 0.000) for 3176 atoms. Found 17 (20 requested) and removed 24 (10 requested) atoms. Cycle 2: After refmac, R = 0.2221 (Rfree = 0.000) for 3139 atoms. Found 12 (20 requested) and removed 23 (10 requested) atoms. Cycle 3: After refmac, R = 0.1977 (Rfree = 0.000) for 3115 atoms. Found 6 (20 requested) and removed 16 (10 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2243 (Rfree = 0.000) for 3096 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 5: After refmac, R = 0.2193 (Rfree = 0.000) for 3083 atoms. Found 15 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.58 Search for helices and strands: 0 residues in 0 chains, 3192 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3209 seeds are put forward Round 1: 188 peptides, 33 chains. Longest chain 15 peptides. Score 0.396 Round 2: 202 peptides, 29 chains. Longest chain 15 peptides. Score 0.504 Round 3: 222 peptides, 32 chains. Longest chain 15 peptides. Score 0.526 Round 4: 229 peptides, 30 chains. Longest chain 26 peptides. Score 0.573 Round 5: 228 peptides, 33 chains. Longest chain 14 peptides. Score 0.530 Taking the results from Round 4 Chains 30, Residues 199, Estimated correctness of the model 3.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7207 restraints for refining 3149 atoms. 6441 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2258 (Rfree = 0.000) for 3149 atoms. Found 14 (20 requested) and removed 27 (10 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2191 (Rfree = 0.000) for 3112 atoms. Found 14 (20 requested) and removed 69 (10 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1926 (Rfree = 0.000) for 3055 atoms. Found 13 (19 requested) and removed 12 (9 requested) atoms. Cycle 9: After refmac, R = 0.1920 (Rfree = 0.000) for 3050 atoms. Found 7 (19 requested) and removed 14 (9 requested) atoms. Cycle 10: After refmac, R = 0.1818 (Rfree = 0.000) for 3040 atoms. Found 5 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.54 Search for helices and strands: 0 residues in 0 chains, 3149 seeds are put forward NCS extension: 43 residues added (3 deleted due to clashes), 3192 seeds are put forward Round 1: 204 peptides, 37 chains. Longest chain 9 peptides. Score 0.392 Round 2: 229 peptides, 34 chains. Longest chain 14 peptides. Score 0.520 Round 3: 243 peptides, 33 chains. Longest chain 19 peptides. Score 0.575 Round 4: 228 peptides, 34 chains. Longest chain 20 peptides. Score 0.517 Round 5: 231 peptides, 32 chains. Longest chain 21 peptides. Score 0.553 Taking the results from Round 3 Chains 35, Residues 210, Estimated correctness of the model 4.6 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7049 restraints for refining 3177 atoms. 6189 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2222 (Rfree = 0.000) for 3177 atoms. Found 16 (20 requested) and removed 18 (10 requested) atoms. Cycle 12: After refmac, R = 0.2209 (Rfree = 0.000) for 3148 atoms. Found 18 (20 requested) and removed 24 (10 requested) atoms. Cycle 13: After refmac, R = 0.1965 (Rfree = 0.000) for 3122 atoms. Found 10 (20 requested) and removed 21 (10 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1934 (Rfree = 0.000) for 3098 atoms. Found 6 (19 requested) and removed 16 (9 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1826 (Rfree = 0.000) for 3080 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.54 Search for helices and strands: 0 residues in 0 chains, 3178 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 3206 seeds are put forward Round 1: 190 peptides, 35 chains. Longest chain 10 peptides. Score 0.371 Round 2: 211 peptides, 32 chains. Longest chain 12 peptides. Score 0.491 Round 3: 225 peptides, 34 chains. Longest chain 13 peptides. Score 0.507 Round 4: 225 peptides, 34 chains. Longest chain 16 peptides. Score 0.507 Round 5: 225 peptides, 31 chains. Longest chain 18 peptides. Score 0.548 Taking the results from Round 5 Chains 31, Residues 194, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7232 restraints for refining 3176 atoms. 6464 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2270 (Rfree = 0.000) for 3176 atoms. Found 14 (20 requested) and removed 37 (10 requested) atoms. Cycle 17: After refmac, R = 0.2214 (Rfree = 0.000) for 3139 atoms. Found 11 (20 requested) and removed 41 (10 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1833 (Rfree = 0.000) for 3098 atoms. Found 5 (19 requested) and removed 16 (9 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1863 (Rfree = 0.000) for 3082 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1785 (Rfree = 0.000) for 3071 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.55 Search for helices and strands: 0 residues in 0 chains, 3175 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3193 seeds are put forward Round 1: 185 peptides, 35 chains. Longest chain 9 peptides. Score 0.353 Round 2: 197 peptides, 30 chains. Longest chain 17 peptides. Score 0.473 Round 3: 213 peptides, 31 chains. Longest chain 14 peptides. Score 0.511 Round 4: 204 peptides, 31 chains. Longest chain 16 peptides. Score 0.482 Round 5: 201 peptides, 29 chains. Longest chain 15 peptides. Score 0.501 Taking the results from Round 3 Chains 31, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7236 restraints for refining 3150 atoms. 6539 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2077 (Rfree = 0.000) for 3150 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 22: After refmac, R = 0.2117 (Rfree = 0.000) for 3134 atoms. Found 15 (20 requested) and removed 21 (10 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1852 (Rfree = 0.000) for 3118 atoms. Found 14 (20 requested) and removed 13 (10 requested) atoms. Cycle 24: After refmac, R = 0.1755 (Rfree = 0.000) for 3111 atoms. Found 4 (20 requested) and removed 13 (10 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1744 (Rfree = 0.000) for 3099 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.54 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3209 seeds are put forward Round 1: 184 peptides, 35 chains. Longest chain 11 peptides. Score 0.349 Round 2: 219 peptides, 37 chains. Longest chain 13 peptides. Score 0.445 Round 3: 226 peptides, 33 chains. Longest chain 14 peptides. Score 0.524 Round 4: 218 peptides, 29 chains. Longest chain 21 peptides. Score 0.554 Round 5: 219 peptides, 35 chains. Longest chain 14 peptides. Score 0.474 Taking the results from Round 4 Chains 29, Residues 189, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 6966 restraints for refining 3154 atoms. 6172 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1972 (Rfree = 0.000) for 3154 atoms. Found 12 (20 requested) and removed 20 (10 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1891 (Rfree = 0.000) for 3138 atoms. Found 13 (20 requested) and removed 15 (10 requested) atoms. Cycle 28: After refmac, R = 0.1885 (Rfree = 0.000) for 3135 atoms. Found 11 (20 requested) and removed 16 (10 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1872 (Rfree = 0.000) for 3127 atoms. Found 11 (20 requested) and removed 14 (10 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1540 (Rfree = 0.000) for 3122 atoms. Found 4 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.54 Search for helices and strands: 0 residues in 0 chains, 3202 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 3228 seeds are put forward Round 1: 177 peptides, 33 chains. Longest chain 11 peptides. Score 0.354 Round 2: 211 peptides, 35 chains. Longest chain 16 peptides. Score 0.447 Round 3: 217 peptides, 31 chains. Longest chain 16 peptides. Score 0.524 Round 4: 226 peptides, 34 chains. Longest chain 16 peptides. Score 0.511 Round 5: 226 peptides, 34 chains. Longest chain 16 peptides. Score 0.511 Taking the results from Round 3 Chains 31, Residues 186, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7231 restraints for refining 3177 atoms. 6499 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1922 (Rfree = 0.000) for 3177 atoms. Found 12 (20 requested) and removed 19 (10 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1722 (Rfree = 0.000) for 3163 atoms. Found 10 (20 requested) and removed 14 (10 requested) atoms. Cycle 33: After refmac, R = 0.1823 (Rfree = 0.000) for 3158 atoms. Found 7 (20 requested) and removed 17 (10 requested) atoms. Cycle 34: After refmac, R = 0.1727 (Rfree = 0.000) for 3147 atoms. Found 9 (20 requested) and removed 13 (10 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1573 (Rfree = 0.000) for 3141 atoms. Found 5 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.50 Search for helices and strands: 0 residues in 0 chains, 3233 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 3260 seeds are put forward Round 1: 190 peptides, 37 chains. Longest chain 12 peptides. Score 0.339 Round 2: 219 peptides, 36 chains. Longest chain 13 peptides. Score 0.459 Round 3: 226 peptides, 37 chains. Longest chain 15 peptides. Score 0.468 Round 4: 228 peptides, 36 chains. Longest chain 13 peptides. Score 0.489 Round 5: 204 peptides, 32 chains. Longest chain 13 peptides. Score 0.467 Taking the results from Round 4 Chains 36, Residues 192, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5411 reflections ( 99.69 % complete ) and 7328 restraints for refining 3177 atoms. 6596 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1903 (Rfree = 0.000) for 3177 atoms. Found 19 (20 requested) and removed 20 (10 requested) atoms. Cycle 37: After refmac, R = 0.1768 (Rfree = 0.000) for 3171 atoms. Found 13 (20 requested) and removed 15 (10 requested) atoms. Cycle 38: After refmac, R = 0.1740 (Rfree = 0.000) for 3167 atoms. Found 17 (20 requested) and removed 14 (10 requested) atoms. Cycle 39: After refmac, R = 0.1861 (Rfree = 0.000) for 3169 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1601 (Rfree = 0.000) for 3163 atoms. Found 8 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.51 Search for helices and strands: 0 residues in 0 chains, 3230 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3246 seeds are put forward Round 1: 149 peptides, 30 chains. Longest chain 10 peptides. Score 0.294 Round 2: 169 peptides, 28 chains. Longest chain 12 peptides. Score 0.405 Round 3: 177 peptides, 31 chains. Longest chain 11 peptides. Score 0.387 Round 4: 162 peptides, 25 chains. Longest chain 12 peptides. Score 0.428 Round 5: 179 peptides, 30 chains. Longest chain 13 peptides. Score 0.410 Taking the results from Round 4 Chains 25, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7508 restraints for refining 3177 atoms. 6985 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1844 (Rfree = 0.000) for 3177 atoms. Found 18 (20 requested) and removed 13 (10 requested) atoms. Cycle 42: After refmac, R = 0.1764 (Rfree = 0.000) for 3179 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1598 (Rfree = 0.000) for 3185 atoms. Found 14 (20 requested) and removed 23 (10 requested) atoms. Cycle 44: After refmac, R = 0.1651 (Rfree = 0.000) for 3173 atoms. Found 16 (20 requested) and removed 15 (10 requested) atoms. Cycle 45: After refmac, R = 0.1541 (Rfree = 0.000) for 3171 atoms. Found 11 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.54 Search for helices and strands: 0 residues in 0 chains, 3242 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3256 seeds are put forward Round 1: 140 peptides, 28 chains. Longest chain 10 peptides. Score 0.291 Round 2: 159 peptides, 29 chains. Longest chain 11 peptides. Score 0.351 Round 3: 151 peptides, 27 chains. Longest chain 10 peptides. Score 0.353 Round 4: 158 peptides, 26 chains. Longest chain 10 peptides. Score 0.397 Round 5: 159 peptides, 26 chains. Longest chain 9 peptides. Score 0.401 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vlm-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5411 reflections ( 99.69 % complete ) and 7459 restraints for refining 3177 atoms. 6953 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1715 (Rfree = 0.000) for 3177 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1717 (Rfree = 0.000) for 3159 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1713 (Rfree = 0.000) for 3144 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1655 (Rfree = 0.000) for 3130 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:23:29 GMT 2018 Job finished. TimeTaking 55.54