Sun 23 Dec 22:23:02 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 2a3n-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a3n-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a3n-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-3.8-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/2a3n-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-3.8-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 22:23:12 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/2a3n-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-3.8-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 216 and 0 Target number of residues in the AU: 216 Target solvent content: 0.6599 Checking the provided sequence file Detected sequence length: 355 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 355 Adjusted target solvent content: 0.44 Input MTZ file: 2a3n-3.8-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: 81.220 102.610 49.296 90.000 123.209 90.000 Input sequence file: 2a3n-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2840 target number of atoms Had to go as low as 0.75 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: 56.657 3.801 Wilson plot Bfac: 84.70 3355 reflections ( 99.73 % complete ) and 0 restraints for refining 3132 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3466 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3093 (Rfree = 0.000) for 3132 atoms. Found 14 (17 requested) and removed 48 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.97 Search for helices and strands: 0 residues in 0 chains, 3152 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 9 peptides. Score 0.254 Round 2: 145 peptides, 25 chains. Longest chain 12 peptides. Score 0.401 Round 3: 153 peptides, 24 chains. Longest chain 13 peptides. Score 0.457 Round 4: 167 peptides, 25 chains. Longest chain 13 peptides. Score 0.497 Round 5: 167 peptides, 23 chains. Longest chain 15 peptides. Score 0.533 Taking the results from Round 5 Chains 24, Residues 144, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.73 % complete ) and 5783 restraints for refining 2569 atoms. 5138 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2200 (Rfree = 0.000) for 2569 atoms. Found 9 (14 requested) and removed 24 (7 requested) atoms. Cycle 2: After refmac, R = 0.2155 (Rfree = 0.000) for 2520 atoms. Found 5 (14 requested) and removed 16 (7 requested) atoms. Cycle 3: After refmac, R = 0.2041 (Rfree = 0.000) for 2479 atoms. Found 8 (13 requested) and removed 11 (6 requested) atoms. Cycle 4: After refmac, R = 0.1913 (Rfree = 0.000) for 2457 atoms. Found 8 (13 requested) and removed 14 (6 requested) atoms. Cycle 5: After refmac, R = 0.1907 (Rfree = 0.000) for 2433 atoms. Found 2 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 3.92 Search for helices and strands: 0 residues in 0 chains, 2522 seeds are put forward Round 1: 146 peptides, 27 chains. Longest chain 11 peptides. Score 0.365 Round 2: 142 peptides, 23 chains. Longest chain 12 peptides. Score 0.427 Round 3: 152 peptides, 21 chains. Longest chain 13 peptides. Score 0.509 Round 4: 159 peptides, 23 chains. Longest chain 12 peptides. Score 0.501 Round 5: 158 peptides, 24 chains. Longest chain 14 peptides. Score 0.478 Taking the results from Round 3 Chains 22, Residues 131, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.73 % complete ) and 5835 restraints for refining 2493 atoms. 5297 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1835 (Rfree = 0.000) for 2493 atoms. Found 11 (13 requested) and removed 16 (6 requested) atoms. Cycle 7: After refmac, R = 0.1593 (Rfree = 0.000) for 2473 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 8: After refmac, R = 0.1882 (Rfree = 0.000) for 2456 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.1990 (Rfree = 0.000) for 2452 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 10: After refmac, R = 0.1915 (Rfree = 0.000) for 2446 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.89 Search for helices and strands: 0 residues in 0 chains, 2547 seeds are put forward Round 1: 128 peptides, 24 chains. Longest chain 12 peptides. Score 0.340 Round 2: 156 peptides, 26 chains. Longest chain 15 peptides. Score 0.432 Round 3: 163 peptides, 24 chains. Longest chain 15 peptides. Score 0.499 Round 4: 157 peptides, 27 chains. Longest chain 14 peptides. Score 0.417 Round 5: 178 peptides, 25 chains. Longest chain 20 peptides. Score 0.541 Taking the results from Round 5 Chains 26, Residues 153, Estimated correctness of the model 0.0 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.73 % complete ) and 5578 restraints for refining 2531 atoms. 4880 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1892 (Rfree = 0.000) for 2531 atoms. Found 12 (13 requested) and removed 18 (6 requested) atoms. Cycle 12: After refmac, R = 0.1676 (Rfree = 0.000) for 2497 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. Cycle 13: After refmac, R = 0.1680 (Rfree = 0.000) for 2476 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.1612 (Rfree = 0.000) for 2467 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1595 (Rfree = 0.000) for 2459 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.92 Search for helices and strands: 0 residues in 0 chains, 2548 seeds are put forward Round 1: 126 peptides, 27 chains. Longest chain 13 peptides. Score 0.265 Round 2: 158 peptides, 28 chains. Longest chain 13 peptides. Score 0.402 Round 3: 159 peptides, 25 chains. Longest chain 13 peptides. Score 0.464 Round 4: 152 peptides, 24 chains. Longest chain 14 peptides. Score 0.452 Round 5: 143 peptides, 23 chains. Longest chain 14 peptides. Score 0.432 Taking the results from Round 3 Chains 25, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.73 % complete ) and 5908 restraints for refining 2513 atoms. 5397 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1865 (Rfree = 0.000) for 2513 atoms. Found 9 (13 requested) and removed 11 (6 requested) atoms. Cycle 17: After refmac, R = 0.1785 (Rfree = 0.000) for 2499 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.1665 (Rfree = 0.000) for 2493 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1640 (Rfree = 0.000) for 2484 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1533 (Rfree = 0.000) for 2482 atoms. Found 0 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.94 Search for helices and strands: 0 residues in 0 chains, 2587 seeds are put forward Round 1: 126 peptides, 25 chains. Longest chain 8 peptides. Score 0.308 Round 2: 146 peptides, 27 chains. Longest chain 9 peptides. Score 0.365 Round 3: 146 peptides, 24 chains. Longest chain 13 peptides. Score 0.426 Round 4: 144 peptides, 24 chains. Longest chain 10 peptides. Score 0.416 Round 5: 151 peptides, 25 chains. Longest chain 13 peptides. Score 0.429 Taking the results from Round 5 Chains 25, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.73 % complete ) and 6030 restraints for refining 2568 atoms. 5551 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1970 (Rfree = 0.000) for 2568 atoms. Found 13 (14 requested) and removed 44 (7 requested) atoms. Cycle 22: After refmac, R = 0.1823 (Rfree = 0.000) for 2523 atoms. Found 10 (13 requested) and removed 12 (6 requested) atoms. Cycle 23: After refmac, R = 0.1878 (Rfree = 0.000) for 2510 atoms. Found 10 (13 requested) and removed 11 (6 requested) atoms. Cycle 24: After refmac, R = 0.1545 (Rfree = 0.000) for 2502 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.1626 (Rfree = 0.000) for 2497 atoms. Found 10 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.87 Search for helices and strands: 0 residues in 0 chains, 2607 seeds are put forward Round 1: 127 peptides, 26 chains. Longest chain 11 peptides. Score 0.292 Round 2: 138 peptides, 26 chains. Longest chain 9 peptides. Score 0.347 Round 3: 141 peptides, 24 chains. Longest chain 18 peptides. Score 0.403 Round 4: 154 peptides, 27 chains. Longest chain 12 peptides. Score 0.403 Round 5: 150 peptides, 24 chains. Longest chain 13 peptides. Score 0.443 Taking the results from Round 5 Chains 24, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.73 % complete ) and 6007 restraints for refining 2569 atoms. 5527 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1618 (Rfree = 0.000) for 2569 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 27: After refmac, R = 0.1809 (Rfree = 0.000) for 2546 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 28: After refmac, R = 0.2004 (Rfree = 0.000) for 2528 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 29: After refmac, R = 0.1832 (Rfree = 0.000) for 2510 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.1922 (Rfree = 0.000) for 2504 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.86 Search for helices and strands: 0 residues in 0 chains, 2608 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 10 peptides. Score 0.255 Round 2: 128 peptides, 25 chains. Longest chain 9 peptides. Score 0.319 Round 3: 122 peptides, 22 chains. Longest chain 11 peptides. Score 0.353 Round 4: 118 peptides, 22 chains. Longest chain 10 peptides. Score 0.333 Round 5: 118 peptides, 19 chains. Longest chain 13 peptides. Score 0.397 Taking the results from Round 5 Chains 21, Residues 99, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.73 % complete ) and 6049 restraints for refining 2533 atoms. 5633 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1829 (Rfree = 0.000) for 2533 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 32: After refmac, R = 0.2015 (Rfree = 0.000) for 2515 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 33: After refmac, R = 0.1773 (Rfree = 0.000) for 2505 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.1172 (Rfree = 0.000) for 2506 atoms. Found 7 (13 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1049 (Rfree = 0.000) for 2507 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.89 Search for helices and strands: 0 residues in 0 chains, 2585 seeds are put forward Round 1: 98 peptides, 22 chains. Longest chain 9 peptides. Score 0.225 Round 2: 121 peptides, 24 chains. Longest chain 11 peptides. Score 0.304 Round 3: 132 peptides, 25 chains. Longest chain 12 peptides. Score 0.339 Round 4: 120 peptides, 22 chains. Longest chain 14 peptides. Score 0.343 Round 5: 115 peptides, 22 chains. Longest chain 10 peptides. Score 0.317 Taking the results from Round 4 Chains 22, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.73 % complete ) and 5931 restraints for refining 2498 atoms. 5561 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1813 (Rfree = 0.000) for 2498 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 37: After refmac, R = 0.1747 (Rfree = 0.000) for 2488 atoms. Found 12 (13 requested) and removed 11 (6 requested) atoms. Cycle 38: After refmac, R = 0.1251 (Rfree = 0.000) for 2480 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.1081 (Rfree = 0.000) for 2472 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1081 (Rfree = 0.000) for 2465 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 3.92 Search for helices and strands: 0 residues in 0 chains, 2561 seeds are put forward Round 1: 98 peptides, 21 chains. Longest chain 9 peptides. Score 0.249 Round 2: 126 peptides, 25 chains. Longest chain 15 peptides. Score 0.308 Round 3: 134 peptides, 26 chains. Longest chain 11 peptides. Score 0.327 Round 4: 145 peptides, 26 chains. Longest chain 10 peptides. Score 0.381 Round 5: 148 peptides, 22 chains. Longest chain 15 peptides. Score 0.473 Taking the results from Round 5 Chains 22, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.73 % complete ) and 5849 restraints for refining 2536 atoms. 5367 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1532 (Rfree = 0.000) for 2536 atoms. Found 12 (13 requested) and removed 9 (6 requested) atoms. Cycle 42: After refmac, R = 0.1755 (Rfree = 0.000) for 2531 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 43: After refmac, R = 0.1960 (Rfree = 0.000) for 2522 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 44: After refmac, R = 0.1729 (Rfree = 0.000) for 2516 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 45: After refmac, R = 0.1572 (Rfree = 0.000) for 2515 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.92 Search for helices and strands: 0 residues in 0 chains, 2622 seeds are put forward Round 1: 98 peptides, 22 chains. Longest chain 6 peptides. Score 0.225 Round 2: 101 peptides, 21 chains. Longest chain 7 peptides. Score 0.265 Round 3: 116 peptides, 22 chains. Longest chain 9 peptides. Score 0.322 Round 4: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.336 Round 5: 106 peptides, 20 chains. Longest chain 8 peptides. Score 0.315 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 90, 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 2a3n-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3355 reflections ( 99.73 % complete ) and 5967 restraints for refining 2537 atoms. 5627 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1784 (Rfree = 0.000) for 2537 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2022 (Rfree = 0.000) for 2521 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1748 (Rfree = 0.000) for 2508 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1692 (Rfree = 0.000) for 2496 atoms. TimeTaking 48.68