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 2ghs-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ghs-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ghs-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-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/2ghs-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-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/2ghs-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-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 195 and 0 Target number of residues in the AU: 195 Target solvent content: 0.6304 Checking the provided sequence file Detected sequence length: 326 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 326 Adjusted target solvent content: 0.38 Input MTZ file: 2ghs-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: 19 Cell parameters: 46.258 75.703 81.538 90.000 90.000 90.000 Input sequence file: 2ghs-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 0.60 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 Loops will be built when appropriate and at the last cycle Resolution range: 55.478 3.600 Wilson plot Bfac: 66.49 3561 reflections ( 99.25 % complete ) and 0 restraints for refining 2894 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3332 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2943 (Rfree = 0.000) for 2894 atoms. Found 18 (18 requested) and removed 51 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.94 Search for helices and strands: 0 residues in 0 chains, 2895 seeds are put forward Round 1: 109 peptides, 23 chains. Longest chain 7 peptides. Score 0.277 Round 2: 160 peptides, 29 chains. Longest chain 14 peptides. Score 0.425 Round 3: 167 peptides, 24 chains. Longest chain 20 peptides. Score 0.563 Round 4: 157 peptides, 25 chains. Longest chain 11 peptides. Score 0.497 Round 5: 166 peptides, 25 chains. Longest chain 13 peptides. Score 0.539 Taking the results from Round 3 Chains 26, Residues 143, Estimated correctness of the model 0.0 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.25 % complete ) and 5283 restraints for refining 2363 atoms. 4648 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2503 (Rfree = 0.000) for 2363 atoms. Found 8 (15 requested) and removed 23 (7 requested) atoms. Cycle 2: After refmac, R = 0.2331 (Rfree = 0.000) for 2318 atoms. Found 6 (15 requested) and removed 20 (7 requested) atoms. Cycle 3: After refmac, R = 0.2323 (Rfree = 0.000) for 2297 atoms. Found 1 (14 requested) and removed 15 (7 requested) atoms. Cycle 4: After refmac, R = 0.2354 (Rfree = 0.000) for 2277 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.2300 (Rfree = 0.000) for 2271 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.94 Search for helices and strands: 0 residues in 0 chains, 2344 seeds are put forward Round 1: 132 peptides, 28 chains. Longest chain 10 peptides. Score 0.291 Round 2: 145 peptides, 22 chains. Longest chain 11 peptides. Score 0.502 Round 3: 142 peptides, 19 chains. Longest chain 14 peptides. Score 0.550 Round 4: 159 peptides, 20 chains. Longest chain 18 peptides. Score 0.605 Round 5: 165 peptides, 20 chains. Longest chain 19 peptides. Score 0.629 Taking the results from Round 5 Chains 21, Residues 145, Estimated correctness of the model 25.6 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.25 % complete ) and 5472 restraints for refining 2355 atoms. 4885 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2387 (Rfree = 0.000) for 2355 atoms. Found 10 (15 requested) and removed 30 (7 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2222 (Rfree = 0.000) for 2325 atoms. Found 9 (14 requested) and removed 12 (7 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2128 (Rfree = 0.000) for 2316 atoms. Found 6 (14 requested) and removed 12 (7 requested) atoms. Cycle 9: After refmac, R = 0.2108 (Rfree = 0.000) for 2305 atoms. Found 3 (14 requested) and removed 11 (7 requested) atoms. Cycle 10: After refmac, R = 0.2039 (Rfree = 0.000) for 2295 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 4.01 Search for helices and strands: 0 residues in 0 chains, 2339 seeds are put forward Round 1: 118 peptides, 23 chains. Longest chain 9 peptides. Score 0.332 Round 2: 146 peptides, 22 chains. Longest chain 17 peptides. Score 0.506 Round 3: 157 peptides, 22 chains. Longest chain 17 peptides. Score 0.558 Round 4: 146 peptides, 19 chains. Longest chain 16 peptides. Score 0.568 Round 5: 141 peptides, 20 chains. Longest chain 14 peptides. Score 0.525 Taking the results from Round 4 Chains 21, Residues 127, Estimated correctness of the model 1.7 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.25 % complete ) and 5415 restraints for refining 2349 atoms. 4831 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2267 (Rfree = 0.000) for 2349 atoms. Found 10 (15 requested) and removed 15 (7 requested) atoms. Cycle 12: After refmac, R = 0.2122 (Rfree = 0.000) for 2341 atoms. Found 2 (15 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2057 (Rfree = 0.000) for 2327 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 14: After refmac, R = 0.1975 (Rfree = 0.000) for 2321 atoms. Found 2 (14 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1918 (Rfree = 0.000) for 2308 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 2354 seeds are put forward Round 1: 130 peptides, 25 chains. Longest chain 10 peptides. Score 0.353 Round 2: 137 peptides, 22 chains. Longest chain 12 peptides. Score 0.461 Round 3: 144 peptides, 22 chains. Longest chain 13 peptides. Score 0.497 Round 4: 144 peptides, 22 chains. Longest chain 13 peptides. Score 0.497 Round 5: 148 peptides, 21 chains. Longest chain 17 peptides. Score 0.537 Taking the results from Round 5 Chains 23, Residues 127, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3561 reflections ( 99.25 % complete ) and 5389 restraints for refining 2353 atoms. 4823 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2238 (Rfree = 0.000) for 2353 atoms. Found 9 (15 requested) and removed 21 (7 requested) atoms. Cycle 17: After refmac, R = 0.2078 (Rfree = 0.000) for 2336 atoms. Found 5 (15 requested) and removed 17 (7 requested) atoms. Cycle 18: After refmac, R = 0.2217 (Rfree = 0.000) for 2314 atoms. Found 11 (14 requested) and removed 10 (7 requested) atoms. Cycle 19: After refmac, R = 0.2031 (Rfree = 0.000) for 2309 atoms. Found 6 (14 requested) and removed 16 (7 requested) atoms. Cycle 20: After refmac, R = 0.1739 (Rfree = 0.000) for 2292 atoms. Found 5 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 2350 seeds are put forward Round 1: 126 peptides, 24 chains. Longest chain 12 peptides. Score 0.354 Round 2: 143 peptides, 25 chains. Longest chain 12 peptides. Score 0.425 Round 3: 147 peptides, 24 chains. Longest chain 11 peptides. Score 0.468 Round 4: 147 peptides, 20 chains. Longest chain 14 peptides. Score 0.553 Round 5: 155 peptides, 21 chains. Longest chain 15 peptides. Score 0.569 Taking the results from Round 5 Chains 23, Residues 134, Estimated correctness of the model 2.2 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.25 % complete ) and 5344 restraints for refining 2343 atoms. 4773 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2173 (Rfree = 0.000) for 2343 atoms. Found 8 (15 requested) and removed 13 (7 requested) atoms. Cycle 22: After refmac, R = 0.2115 (Rfree = 0.000) for 2331 atoms. Found 11 (14 requested) and removed 16 (7 requested) atoms. Cycle 23: After refmac, R = 0.1802 (Rfree = 0.000) for 2317 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1717 (Rfree = 0.000) for 2306 atoms. Found 4 (14 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.1684 (Rfree = 0.000) for 2296 atoms. Found 0 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.97 Search for helices and strands: 0 residues in 0 chains, 2346 seeds are put forward Round 1: 131 peptides, 24 chains. Longest chain 11 peptides. Score 0.383 Round 2: 152 peptides, 23 chains. Longest chain 21 peptides. Score 0.514 Round 3: 157 peptides, 26 chains. Longest chain 12 peptides. Score 0.475 Round 4: 151 peptides, 23 chains. Longest chain 20 peptides. Score 0.510 Round 5: 147 peptides, 23 chains. Longest chain 14 peptides. Score 0.490 Taking the results from Round 2 Chains 23, Residues 129, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3561 reflections ( 99.25 % complete ) and 5370 restraints for refining 2287 atoms. 4841 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2038 (Rfree = 0.000) for 2287 atoms. Found 13 (14 requested) and removed 8 (7 requested) atoms. Cycle 27: After refmac, R = 0.1954 (Rfree = 0.000) for 2287 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2017 (Rfree = 0.000) for 2280 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 29: After refmac, R = 0.1934 (Rfree = 0.000) for 2272 atoms. Found 4 (14 requested) and removed 10 (7 requested) atoms. Cycle 30: After refmac, R = 0.1854 (Rfree = 0.000) for 2265 atoms. Found 2 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.98 Search for helices and strands: 0 residues in 0 chains, 2328 seeds are put forward Round 1: 129 peptides, 25 chains. Longest chain 10 peptides. Score 0.347 Round 2: 133 peptides, 20 chains. Longest chain 12 peptides. Score 0.486 Round 3: 142 peptides, 20 chains. Longest chain 12 peptides. Score 0.529 Round 4: 141 peptides, 23 chains. Longest chain 11 peptides. Score 0.460 Round 5: 144 peptides, 22 chains. Longest chain 17 peptides. Score 0.497 Taking the results from Round 3 Chains 20, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.25 % complete ) and 5597 restraints for refining 2337 atoms. 5129 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2126 (Rfree = 0.000) for 2337 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. Cycle 32: After refmac, R = 0.2082 (Rfree = 0.000) for 2326 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. Cycle 33: After refmac, R = 0.1726 (Rfree = 0.000) for 2324 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.1728 (Rfree = 0.000) for 2320 atoms. Found 0 (14 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1697 (Rfree = 0.000) for 2312 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 4.01 Search for helices and strands: 0 residues in 0 chains, 2366 seeds are put forward Round 1: 109 peptides, 20 chains. Longest chain 11 peptides. Score 0.354 Round 2: 132 peptides, 20 chains. Longest chain 12 peptides. Score 0.480 Round 3: 148 peptides, 24 chains. Longest chain 14 peptides. Score 0.473 Round 4: 144 peptides, 20 chains. Longest chain 14 peptides. Score 0.539 Round 5: 147 peptides, 20 chains. Longest chain 13 peptides. Score 0.553 Taking the results from Round 5 Chains 20, Residues 127, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3561 reflections ( 99.25 % complete ) and 5538 restraints for refining 2364 atoms. 4989 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1975 (Rfree = 0.000) for 2364 atoms. Found 7 (15 requested) and removed 18 (7 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1979 (Rfree = 0.000) for 2347 atoms. Found 7 (15 requested) and removed 11 (7 requested) atoms. Cycle 38: After refmac, R = 0.2002 (Rfree = 0.000) for 2338 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1618 (Rfree = 0.000) for 2329 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1580 (Rfree = 0.000) for 2325 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.94 Search for helices and strands: 0 residues in 0 chains, 2364 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 7 peptides. Score 0.272 Round 2: 131 peptides, 23 chains. Longest chain 14 peptides. Score 0.406 Round 3: 137 peptides, 23 chains. Longest chain 12 peptides. Score 0.439 Round 4: 123 peptides, 21 chains. Longest chain 13 peptides. Score 0.410 Round 5: 139 peptides, 22 chains. Longest chain 10 peptides. Score 0.472 Taking the results from Round 5 Chains 22, Residues 117, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.25 % complete ) and 5743 restraints for refining 2364 atoms. 5278 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2062 (Rfree = 0.000) for 2364 atoms. Found 7 (15 requested) and removed 18 (7 requested) atoms. Cycle 42: After refmac, R = 0.1989 (Rfree = 0.000) for 2341 atoms. Found 6 (15 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2063 (Rfree = 0.000) for 2331 atoms. Found 10 (14 requested) and removed 10 (7 requested) atoms. Cycle 44: After refmac, R = 0.1747 (Rfree = 0.000) for 2328 atoms. Found 0 (14 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1747 (Rfree = 0.000) for 2318 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.94 Search for helices and strands: 0 residues in 0 chains, 2376 seeds are put forward Round 1: 106 peptides, 23 chains. Longest chain 8 peptides. Score 0.259 Round 2: 113 peptides, 22 chains. Longest chain 7 peptides. Score 0.327 Round 3: 111 peptides, 19 chains. Longest chain 8 peptides. Score 0.391 Round 4: 113 peptides, 19 chains. Longest chain 9 peptides. Score 0.402 Round 5: 100 peptides, 17 chains. Longest chain 12 peptides. Score 0.377 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 94, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2ghs-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 235 A and 246 A 18 chains (101 residues) following loop building 3 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3561 reflections ( 99.25 % complete ) and 5602 restraints for refining 2364 atoms. 5130 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1902 (Rfree = 0.000) for 2364 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1772 (Rfree = 0.000) for 2351 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1700 (Rfree = 0.000) for 2340 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1655 (Rfree = 0.000) for 2327 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:13:55 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 45.99