null Tue 25 Dec 19:27:56 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 2pn1-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pn1-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pn1-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-3.2-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/2pn1-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-3.2-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 19:28:10 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/2pn1-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-3.2-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 251 and 0 Target number of residues in the AU: 251 Target solvent content: 0.6182 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 331 Adjusted target solvent content: 0.50 Input MTZ file: 2pn1-3.2-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: 5 Cell parameters: 91.460 61.130 76.770 90.000 124.022 90.000 Input sequence file: 2pn1-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2648 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 Loops will be built when appropriate and at the last cycle Resolution range: 63.629 3.200 Wilson plot Bfac: 59.96 5673 reflections ( 96.12 % complete ) and 0 restraints for refining 2937 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3469 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3018 (Rfree = 0.000) for 2937 atoms. Found 19 (26 requested) and removed 45 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.16 Search for helices and strands: 0 residues in 0 chains, 2959 seeds are put forward Round 1: 139 peptides, 28 chains. Longest chain 11 peptides. Score 0.307 Round 2: 171 peptides, 31 chains. Longest chain 13 peptides. Score 0.397 Round 3: 161 peptides, 29 chains. Longest chain 15 peptides. Score 0.390 Round 4: 168 peptides, 28 chains. Longest chain 13 peptides. Score 0.440 Round 5: 165 peptides, 27 chains. Longest chain 13 peptides. Score 0.445 Taking the results from Round 5 Chains 30, Residues 138, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 5673 reflections ( 96.12 % complete ) and 5374 restraints for refining 2418 atoms. 4789 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2457 (Rfree = 0.000) for 2418 atoms. Found 18 (21 requested) and removed 22 (10 requested) atoms. Cycle 2: After refmac, R = 0.2237 (Rfree = 0.000) for 2402 atoms. Found 8 (21 requested) and removed 13 (10 requested) atoms. Cycle 3: After refmac, R = 0.2185 (Rfree = 0.000) for 2385 atoms. Found 5 (21 requested) and removed 12 (10 requested) atoms. Cycle 4: After refmac, R = 0.2121 (Rfree = 0.000) for 2375 atoms. Found 5 (21 requested) and removed 13 (10 requested) atoms. Cycle 5: After refmac, R = 0.2058 (Rfree = 0.000) for 2361 atoms. Found 4 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.07 3.07 Search for helices and strands: 0 residues in 0 chains, 2433 seeds are put forward Round 1: 151 peptides, 30 chains. Longest chain 13 peptides. Score 0.324 Round 2: 161 peptides, 26 chains. Longest chain 19 peptides. Score 0.447 Round 3: 161 peptides, 28 chains. Longest chain 12 peptides. Score 0.409 Round 4: 159 peptides, 25 chains. Longest chain 14 peptides. Score 0.457 Round 5: 172 peptides, 27 chains. Longest chain 19 peptides. Score 0.474 Taking the results from Round 5 Chains 29, Residues 145, Estimated correctness of the model 2.7 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5673 reflections ( 96.12 % complete ) and 5345 restraints for refining 2418 atoms. 4742 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2301 (Rfree = 0.000) for 2418 atoms. Found 19 (21 requested) and removed 19 (10 requested) atoms. Cycle 7: After refmac, R = 0.2119 (Rfree = 0.000) for 2415 atoms. Found 10 (21 requested) and removed 12 (10 requested) atoms. Cycle 8: After refmac, R = 0.2062 (Rfree = 0.000) for 2409 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 9: After refmac, R = 0.2007 (Rfree = 0.000) for 2403 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 10: After refmac, R = 0.1956 (Rfree = 0.000) for 2397 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 3.09 Search for helices and strands: 0 residues in 0 chains, 2452 seeds are put forward Round 1: 138 peptides, 29 chains. Longest chain 11 peptides. Score 0.281 Round 2: 150 peptides, 26 chains. Longest chain 14 peptides. Score 0.398 Round 3: 152 peptides, 26 chains. Longest chain 11 peptides. Score 0.407 Round 4: 159 peptides, 27 chains. Longest chain 12 peptides. Score 0.419 Round 5: 167 peptides, 28 chains. Longest chain 12 peptides. Score 0.435 Taking the results from Round 5 Chains 28, Residues 139, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5673 reflections ( 96.12 % complete ) and 5465 restraints for refining 2418 atoms. 4909 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2260 (Rfree = 0.000) for 2418 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 12: After refmac, R = 0.2142 (Rfree = 0.000) for 2413 atoms. Found 14 (21 requested) and removed 10 (10 requested) atoms. Cycle 13: After refmac, R = 0.2069 (Rfree = 0.000) for 2416 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. Cycle 14: After refmac, R = 0.2013 (Rfree = 0.000) for 2409 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. Cycle 15: After refmac, R = 0.2333 (Rfree = 0.000) for 2398 atoms. Found 12 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 3.07 Search for helices and strands: 0 residues in 0 chains, 2466 seeds are put forward Round 1: 148 peptides, 26 chains. Longest chain 12 peptides. Score 0.389 Round 2: 180 peptides, 30 chains. Longest chain 13 peptides. Score 0.454 Round 3: 192 peptides, 32 chains. Longest chain 13 peptides. Score 0.468 Round 4: 168 peptides, 28 chains. Longest chain 13 peptides. Score 0.440 Round 5: 185 peptides, 27 chains. Longest chain 13 peptides. Score 0.526 Taking the results from Round 5 Chains 28, Residues 158, Estimated correctness of the model 19.6 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5673 reflections ( 96.12 % complete ) and 5290 restraints for refining 2418 atoms. 4660 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2174 (Rfree = 0.000) for 2418 atoms. Found 19 (21 requested) and removed 13 (10 requested) atoms. Cycle 17: After refmac, R = 0.2011 (Rfree = 0.000) for 2419 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. Cycle 18: After refmac, R = 0.1984 (Rfree = 0.000) for 2413 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 19: After refmac, R = 0.2333 (Rfree = 0.000) for 2405 atoms. Found 14 (21 requested) and removed 10 (10 requested) atoms. Cycle 20: After refmac, R = 0.1984 (Rfree = 0.000) for 2407 atoms. Found 1 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 3.13 Search for helices and strands: 0 residues in 0 chains, 2450 seeds are put forward Round 1: 142 peptides, 27 chains. Longest chain 12 peptides. Score 0.342 Round 2: 156 peptides, 25 chains. Longest chain 12 peptides. Score 0.444 Round 3: 160 peptides, 26 chains. Longest chain 12 peptides. Score 0.442 Round 4: 162 peptides, 23 chains. Longest chain 16 peptides. Score 0.505 Round 5: 159 peptides, 24 chains. Longest chain 12 peptides. Score 0.475 Taking the results from Round 4 Chains 23, Residues 139, Estimated correctness of the model 12.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5673 reflections ( 96.12 % complete ) and 5394 restraints for refining 2416 atoms. 4861 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2049 (Rfree = 0.000) for 2416 atoms. Found 13 (21 requested) and removed 12 (10 requested) atoms. Cycle 22: After refmac, R = 0.1962 (Rfree = 0.000) for 2415 atoms. Found 9 (21 requested) and removed 11 (10 requested) atoms. Cycle 23: After refmac, R = 0.1858 (Rfree = 0.000) for 2411 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. Cycle 24: After refmac, R = 0.1794 (Rfree = 0.000) for 2405 atoms. Found 9 (21 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.1745 (Rfree = 0.000) for 2402 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 3.11 Search for helices and strands: 0 residues in 0 chains, 2468 seeds are put forward Round 1: 136 peptides, 28 chains. Longest chain 11 peptides. Score 0.292 Round 2: 155 peptides, 27 chains. Longest chain 10 peptides. Score 0.402 Round 3: 158 peptides, 26 chains. Longest chain 12 peptides. Score 0.434 Round 4: 160 peptides, 28 chains. Longest chain 12 peptides. Score 0.405 Round 5: 168 peptides, 26 chains. Longest chain 12 peptides. Score 0.476 Taking the results from Round 5 Chains 26, Residues 142, Estimated correctness of the model 3.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5673 reflections ( 96.12 % complete ) and 5470 restraints for refining 2418 atoms. 4928 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1939 (Rfree = 0.000) for 2418 atoms. Found 19 (21 requested) and removed 10 (10 requested) atoms. Cycle 27: After refmac, R = 0.1783 (Rfree = 0.000) for 2421 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.1871 (Rfree = 0.000) for 2413 atoms. Found 9 (21 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.2255 (Rfree = 0.000) for 2412 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.1640 (Rfree = 0.000) for 2417 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.13 Search for helices and strands: 0 residues in 0 chains, 2476 seeds are put forward Round 1: 128 peptides, 25 chains. Longest chain 12 peptides. Score 0.315 Round 2: 158 peptides, 26 chains. Longest chain 13 peptides. Score 0.434 Round 3: 167 peptides, 26 chains. Longest chain 13 peptides. Score 0.472 Round 4: 164 peptides, 25 chains. Longest chain 11 peptides. Score 0.477 Round 5: 161 peptides, 24 chains. Longest chain 12 peptides. Score 0.483 Taking the results from Round 5 Chains 25, Residues 137, Estimated correctness of the model 5.7 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5673 reflections ( 96.12 % complete ) and 5232 restraints for refining 2418 atoms. 4656 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1977 (Rfree = 0.000) for 2418 atoms. Found 11 (21 requested) and removed 12 (10 requested) atoms. Cycle 32: After refmac, R = 0.1801 (Rfree = 0.000) for 2414 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. Cycle 33: After refmac, R = 0.1862 (Rfree = 0.000) for 2405 atoms. Found 14 (21 requested) and removed 11 (10 requested) atoms. Cycle 34: After refmac, R = 0.2006 (Rfree = 0.000) for 2405 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.1739 (Rfree = 0.000) for 2413 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.13 Search for helices and strands: 0 residues in 0 chains, 2453 seeds are put forward Round 1: 122 peptides, 25 chains. Longest chain 11 peptides. Score 0.285 Round 2: 149 peptides, 24 chains. Longest chain 10 peptides. Score 0.432 Round 3: 162 peptides, 25 chains. Longest chain 11 peptides. Score 0.469 Round 4: 154 peptides, 22 chains. Longest chain 15 peptides. Score 0.491 Round 5: 160 peptides, 24 chains. Longest chain 11 peptides. Score 0.479 Taking the results from Round 4 Chains 22, Residues 132, Estimated correctness of the model 8.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5673 reflections ( 96.12 % complete ) and 5429 restraints for refining 2417 atoms. 4923 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2373 (Rfree = 0.000) for 2417 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. Cycle 37: After refmac, R = 0.2057 (Rfree = 0.000) for 2424 atoms. Found 20 (21 requested) and removed 11 (10 requested) atoms. Cycle 38: After refmac, R = 0.2097 (Rfree = 0.000) for 2433 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.1680 (Rfree = 0.000) for 2437 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1688 (Rfree = 0.000) for 2430 atoms. Found 9 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.08 3.08 Search for helices and strands: 0 residues in 0 chains, 2488 seeds are put forward Round 1: 116 peptides, 21 chains. Longest chain 12 peptides. Score 0.340 Round 2: 130 peptides, 19 chains. Longest chain 16 peptides. Score 0.446 Round 3: 148 peptides, 22 chains. Longest chain 18 peptides. Score 0.466 Round 4: 134 peptides, 23 chains. Longest chain 12 peptides. Score 0.385 Round 5: 154 peptides, 23 chains. Longest chain 18 peptides. Score 0.472 Taking the results from Round 5 Chains 24, Residues 131, Estimated correctness of the model 2.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5673 reflections ( 96.12 % complete ) and 5136 restraints for refining 2418 atoms. 4556 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1941 (Rfree = 0.000) for 2418 atoms. Found 18 (21 requested) and removed 12 (10 requested) atoms. Cycle 42: After refmac, R = 0.1867 (Rfree = 0.000) for 2415 atoms. Found 11 (21 requested) and removed 12 (10 requested) atoms. Cycle 43: After refmac, R = 0.1732 (Rfree = 0.000) for 2405 atoms. Found 6 (21 requested) and removed 11 (10 requested) atoms. Cycle 44: After refmac, R = 0.2234 (Rfree = 0.000) for 2393 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. Cycle 45: After refmac, R = 0.1752 (Rfree = 0.000) for 2398 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.09 Search for helices and strands: 0 residues in 0 chains, 2440 seeds are put forward Round 1: 117 peptides, 21 chains. Longest chain 10 peptides. Score 0.345 Round 2: 126 peptides, 21 chains. Longest chain 15 peptides. Score 0.388 Round 3: 111 peptides, 18 chains. Longest chain 14 peptides. Score 0.380 Round 4: 108 peptides, 18 chains. Longest chain 14 peptides. Score 0.365 Round 5: 107 peptides, 17 chains. Longest chain 9 peptides. Score 0.382 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 105, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2pn1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5673 reflections ( 96.12 % complete ) and 5458 restraints for refining 2417 atoms. 5031 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2069 (Rfree = 0.000) for 2417 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1809 (Rfree = 0.000) for 2403 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1992 (Rfree = 0.000) for 2391 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1780 (Rfree = 0.000) for 2381 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:26:11 GMT 2018 Job finished. TimeTaking 58.27 Used memory is bytes: 7852088