Sun 23 Dec 22:22:50 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 2pn1-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pn1-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pn1-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-3.4-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/2pn1-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-3.4-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 ============================================================ Sun 23 Dec 22:22:59 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/2pn1-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-3.4-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 246 and 0 Target number of residues in the AU: 246 Target solvent content: 0.6258 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: 2pn1-3.4-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: 2pn1-3.4-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 3.400 Wilson plot Bfac: 63.71 4723 reflections ( 95.63 % complete ) and 0 restraints for refining 2927 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3427 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3787 (Rfree = 0.000) for 2927 atoms. Found 22 (22 requested) and removed 85 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.62 Search for helices and strands: 0 residues in 0 chains, 2906 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 7 peptides. Score 0.219 Round 2: 120 peptides, 25 chains. Longest chain 9 peptides. Score 0.275 Round 3: 137 peptides, 25 chains. Longest chain 10 peptides. Score 0.358 Round 4: 138 peptides, 24 chains. Longest chain 11 peptides. Score 0.383 Round 5: 142 peptides, 23 chains. Longest chain 11 peptides. Score 0.421 Taking the results from Round 5 Chains 23, Residues 119, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4723 reflections ( 95.63 % complete ) and 5597 restraints for refining 2408 atoms. 5115 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3210 (Rfree = 0.000) for 2408 atoms. Found 18 (18 requested) and removed 36 (9 requested) atoms. Cycle 2: After refmac, R = 0.3022 (Rfree = 0.000) for 2348 atoms. Found 18 (18 requested) and removed 24 (9 requested) atoms. Cycle 3: After refmac, R = 0.2557 (Rfree = 0.000) for 2305 atoms. Found 12 (17 requested) and removed 17 (8 requested) atoms. Cycle 4: After refmac, R = 0.2363 (Rfree = 0.000) for 2285 atoms. Found 11 (17 requested) and removed 16 (8 requested) atoms. Cycle 5: After refmac, R = 0.2369 (Rfree = 0.000) for 2276 atoms. Found 14 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.22 Search for helices and strands: 0 residues in 0 chains, 2331 seeds are put forward Round 1: 129 peptides, 26 chains. Longest chain 9 peptides. Score 0.299 Round 2: 166 peptides, 29 chains. Longest chain 17 peptides. Score 0.412 Round 3: 160 peptides, 27 chains. Longest chain 11 peptides. Score 0.424 Round 4: 163 peptides, 27 chains. Longest chain 13 peptides. Score 0.437 Round 5: 169 peptides, 30 chains. Longest chain 12 peptides. Score 0.407 Taking the results from Round 4 Chains 27, Residues 136, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4723 reflections ( 95.63 % complete ) and 5339 restraints for refining 2362 atoms. 4771 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2701 (Rfree = 0.000) for 2362 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 7: After refmac, R = 0.2303 (Rfree = 0.000) for 2337 atoms. Found 16 (17 requested) and removed 12 (8 requested) atoms. Cycle 8: After refmac, R = 0.2138 (Rfree = 0.000) for 2336 atoms. Found 16 (17 requested) and removed 13 (8 requested) atoms. Cycle 9: After refmac, R = 0.2204 (Rfree = 0.000) for 2333 atoms. Found 14 (17 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.2022 (Rfree = 0.000) for 2333 atoms. Found 13 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.19 Search for helices and strands: 0 residues in 0 chains, 2405 seeds are put forward Round 1: 140 peptides, 29 chains. Longest chain 9 peptides. Score 0.291 Round 2: 161 peptides, 27 chains. Longest chain 11 peptides. Score 0.428 Round 3: 169 peptides, 26 chains. Longest chain 16 peptides. Score 0.480 Round 4: 165 peptides, 28 chains. Longest chain 10 peptides. Score 0.427 Round 5: 170 peptides, 30 chains. Longest chain 11 peptides. Score 0.411 Taking the results from Round 3 Chains 27, Residues 143, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4723 reflections ( 95.63 % complete ) and 5306 restraints for refining 2408 atoms. 4696 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2269 (Rfree = 0.000) for 2408 atoms. Found 17 (18 requested) and removed 21 (9 requested) atoms. Cycle 12: After refmac, R = 0.2204 (Rfree = 0.000) for 2386 atoms. Found 14 (18 requested) and removed 15 (9 requested) atoms. Cycle 13: After refmac, R = 0.2053 (Rfree = 0.000) for 2378 atoms. Found 9 (18 requested) and removed 11 (9 requested) atoms. Cycle 14: After refmac, R = 0.1971 (Rfree = 0.000) for 2370 atoms. Found 9 (17 requested) and removed 10 (8 requested) atoms. Cycle 15: After refmac, R = 0.1898 (Rfree = 0.000) for 2365 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 2419 seeds are put forward Round 1: 127 peptides, 27 chains. Longest chain 9 peptides. Score 0.268 Round 2: 148 peptides, 29 chains. Longest chain 9 peptides. Score 0.330 Round 3: 168 peptides, 30 chains. Longest chain 11 peptides. Score 0.402 Round 4: 166 peptides, 27 chains. Longest chain 9 peptides. Score 0.449 Round 5: 174 peptides, 32 chains. Longest chain 13 peptides. Score 0.391 Taking the results from Round 4 Chains 27, Residues 139, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4723 reflections ( 95.63 % complete ) and 5533 restraints for refining 2407 atoms. 4961 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2239 (Rfree = 0.000) for 2407 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 17: After refmac, R = 0.2114 (Rfree = 0.000) for 2393 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 18: After refmac, R = 0.1914 (Rfree = 0.000) for 2389 atoms. Found 5 (18 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.2004 (Rfree = 0.000) for 2373 atoms. Found 13 (18 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.1776 (Rfree = 0.000) for 2367 atoms. Found 16 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 3.18 Search for helices and strands: 0 residues in 0 chains, 2426 seeds are put forward Round 1: 131 peptides, 27 chains. Longest chain 9 peptides. Score 0.288 Round 2: 160 peptides, 28 chains. Longest chain 10 peptides. Score 0.405 Round 3: 167 peptides, 28 chains. Longest chain 12 peptides. Score 0.435 Round 4: 152 peptides, 28 chains. Longest chain 9 peptides. Score 0.369 Round 5: 158 peptides, 26 chains. Longest chain 12 peptides. Score 0.434 Taking the results from Round 3 Chains 28, Residues 139, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4723 reflections ( 95.63 % complete ) and 5444 restraints for refining 2407 atoms. 4866 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2127 (Rfree = 0.000) for 2407 atoms. Found 16 (18 requested) and removed 16 (9 requested) atoms. Cycle 22: After refmac, R = 0.1970 (Rfree = 0.000) for 2396 atoms. Found 12 (18 requested) and removed 18 (9 requested) atoms. Cycle 23: After refmac, R = 0.1843 (Rfree = 0.000) for 2377 atoms. Found 15 (18 requested) and removed 15 (9 requested) atoms. Cycle 24: After refmac, R = 0.1862 (Rfree = 0.000) for 2371 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.1773 (Rfree = 0.000) for 2374 atoms. Found 12 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.18 Search for helices and strands: 0 residues in 0 chains, 2448 seeds are put forward Round 1: 120 peptides, 25 chains. Longest chain 9 peptides. Score 0.275 Round 2: 143 peptides, 28 chains. Longest chain 12 peptides. Score 0.326 Round 3: 141 peptides, 24 chains. Longest chain 10 peptides. Score 0.397 Round 4: 143 peptides, 25 chains. Longest chain 12 peptides. Score 0.386 Round 5: 141 peptides, 24 chains. Longest chain 12 peptides. Score 0.397 Taking the results from Round 5 Chains 24, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4723 reflections ( 95.63 % complete ) and 5638 restraints for refining 2408 atoms. 5194 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2124 (Rfree = 0.000) for 2408 atoms. Found 15 (18 requested) and removed 10 (9 requested) atoms. Cycle 27: After refmac, R = 0.1847 (Rfree = 0.000) for 2397 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 28: After refmac, R = 0.1668 (Rfree = 0.000) for 2394 atoms. Found 9 (18 requested) and removed 11 (9 requested) atoms. Cycle 29: After refmac, R = 0.1543 (Rfree = 0.000) for 2390 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Cycle 30: After refmac, R = 0.1518 (Rfree = 0.000) for 2378 atoms. Found 6 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 3.14 Search for helices and strands: 0 residues in 0 chains, 2425 seeds are put forward Round 1: 115 peptides, 24 chains. Longest chain 8 peptides. Score 0.270 Round 2: 154 peptides, 28 chains. Longest chain 11 peptides. Score 0.378 Round 3: 150 peptides, 26 chains. Longest chain 11 peptides. Score 0.398 Round 4: 150 peptides, 24 chains. Longest chain 13 peptides. Score 0.437 Round 5: 146 peptides, 25 chains. Longest chain 12 peptides. Score 0.400 Taking the results from Round 4 Chains 24, Residues 126, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4723 reflections ( 95.63 % complete ) and 5511 restraints for refining 2408 atoms. 5007 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1814 (Rfree = 0.000) for 2408 atoms. Found 17 (18 requested) and removed 13 (9 requested) atoms. Cycle 32: After refmac, R = 0.1664 (Rfree = 0.000) for 2405 atoms. Found 9 (18 requested) and removed 11 (9 requested) atoms. Cycle 33: After refmac, R = 0.1562 (Rfree = 0.000) for 2402 atoms. Found 8 (18 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.1531 (Rfree = 0.000) for 2397 atoms. Found 2 (18 requested) and removed 12 (9 requested) atoms. Cycle 35: After refmac, R = 0.1496 (Rfree = 0.000) for 2385 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 2442 seeds are put forward Round 1: 122 peptides, 25 chains. Longest chain 8 peptides. Score 0.285 Round 2: 139 peptides, 25 chains. Longest chain 13 peptides. Score 0.368 Round 3: 139 peptides, 26 chains. Longest chain 11 peptides. Score 0.348 Round 4: 142 peptides, 24 chains. Longest chain 11 peptides. Score 0.401 Round 5: 144 peptides, 26 chains. Longest chain 11 peptides. Score 0.371 Taking the results from Round 4 Chains 24, Residues 118, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4723 reflections ( 95.63 % complete ) and 5443 restraints for refining 2408 atoms. 4953 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1858 (Rfree = 0.000) for 2408 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 37: After refmac, R = 0.1841 (Rfree = 0.000) for 2407 atoms. Found 7 (18 requested) and removed 11 (9 requested) atoms. Cycle 38: After refmac, R = 0.1678 (Rfree = 0.000) for 2400 atoms. Found 10 (18 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.1717 (Rfree = 0.000) for 2396 atoms. Found 11 (18 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.1578 (Rfree = 0.000) for 2394 atoms. Found 8 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 2454 seeds are put forward Round 1: 108 peptides, 23 chains. Longest chain 8 peptides. Score 0.256 Round 2: 122 peptides, 22 chains. Longest chain 10 peptides. Score 0.348 Round 3: 130 peptides, 22 chains. Longest chain 12 peptides. Score 0.386 Round 4: 136 peptides, 24 chains. Longest chain 13 peptides. Score 0.374 Round 5: 116 peptides, 21 chains. Longest chain 10 peptides. Score 0.340 Taking the results from Round 3 Chains 23, Residues 108, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4723 reflections ( 95.63 % complete ) and 5409 restraints for refining 2408 atoms. 4933 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1817 (Rfree = 0.000) for 2408 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 42: After refmac, R = 0.1839 (Rfree = 0.000) for 2407 atoms. Found 12 (18 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1490 (Rfree = 0.000) for 2403 atoms. Found 8 (18 requested) and removed 9 (9 requested) atoms. Cycle 44: After refmac, R = 0.1483 (Rfree = 0.000) for 2398 atoms. Found 5 (18 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.1459 (Rfree = 0.000) for 2390 atoms. Found 5 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.18 Search for helices and strands: 0 residues in 0 chains, 2428 seeds are put forward Round 1: 118 peptides, 25 chains. Longest chain 11 peptides. Score 0.264 Round 2: 130 peptides, 25 chains. Longest chain 9 peptides. Score 0.325 Round 3: 129 peptides, 23 chains. Longest chain 9 peptides. Score 0.361 Round 4: 132 peptides, 24 chains. Longest chain 12 peptides. Score 0.355 Round 5: 132 peptides, 24 chains. Longest chain 11 peptides. Score 0.355 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 106, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2pn1-3_warpNtrace.pdb as input Building loops using Loopy2018 23 chains (106 residues) following loop building 2 chains (7 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4723 reflections ( 95.63 % complete ) and 5428 restraints for refining 2408 atoms. 5012 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1711 (Rfree = 0.000) for 2408 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1708 (Rfree = 0.000) for 2393 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1565 (Rfree = 0.000) for 2380 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1561 (Rfree = 0.000) for 2367 atoms. TimeTaking 47.12