Sun 23 Dec 22:22:41 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 1vqz-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqz-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqz-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-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/1vqz-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-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 22:22:50 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/1vqz-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-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 264 and 0 Target number of residues in the AU: 264 Target solvent content: 0.6068 Checking the provided sequence file Detected sequence length: 341 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 341 Adjusted target solvent content: 0.49 Input MTZ file: 1vqz-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: 19 Cell parameters: 45.503 70.280 113.629 90.000 90.000 90.000 Input sequence file: 1vqz-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2728 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: 59.771 3.400 Wilson plot Bfac: 54.98 5372 reflections ( 99.76 % complete ) and 0 restraints for refining 3019 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3243 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2628 (Rfree = 0.000) for 3019 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.06 3.10 Search for helices and strands: 0 residues in 0 chains, 3076 seeds are put forward Round 1: 164 peptides, 29 chains. Longest chain 11 peptides. Score 0.400 Round 2: 203 peptides, 32 chains. Longest chain 13 peptides. Score 0.506 Round 3: 217 peptides, 29 chains. Longest chain 14 peptides. Score 0.601 Round 4: 216 peptides, 28 chains. Longest chain 26 peptides. Score 0.612 Round 5: 215 peptides, 25 chains. Longest chain 19 peptides. Score 0.650 Taking the results from Round 5 Chains 27, Residues 190, Estimated correctness of the model 44.1 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5372 reflections ( 99.76 % complete ) and 5344 restraints for refining 2481 atoms. 4546 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2437 (Rfree = 0.000) for 2481 atoms. Found 14 (18 requested) and removed 15 (9 requested) atoms. Cycle 2: After refmac, R = 0.2241 (Rfree = 0.000) for 2452 atoms. Found 9 (18 requested) and removed 9 (9 requested) atoms. Cycle 3: After refmac, R = 0.2326 (Rfree = 0.000) for 2440 atoms. Found 9 (18 requested) and removed 14 (9 requested) atoms. Cycle 4: After refmac, R = 0.2100 (Rfree = 0.000) for 2428 atoms. Found 8 (18 requested) and removed 15 (9 requested) atoms. Cycle 5: After refmac, R = 0.2013 (Rfree = 0.000) for 2418 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 2502 seeds are put forward Round 1: 189 peptides, 31 chains. Longest chain 15 peptides. Score 0.468 Round 2: 201 peptides, 28 chains. Longest chain 15 peptides. Score 0.562 Round 3: 209 peptides, 25 chains. Longest chain 18 peptides. Score 0.632 Round 4: 218 peptides, 26 chains. Longest chain 33 peptides. Score 0.646 Round 5: 218 peptides, 25 chains. Longest chain 19 peptides. Score 0.659 Taking the results from Round 5 Chains 25, Residues 193, Estimated correctness of the model 46.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5372 reflections ( 99.76 % complete ) and 5516 restraints for refining 2481 atoms. 4769 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2389 (Rfree = 0.000) for 2481 atoms. Found 9 (18 requested) and removed 15 (9 requested) atoms. Cycle 7: After refmac, R = 0.2182 (Rfree = 0.000) for 2466 atoms. Found 5 (18 requested) and removed 10 (9 requested) atoms. Cycle 8: After refmac, R = 0.2094 (Rfree = 0.000) for 2454 atoms. Found 6 (18 requested) and removed 11 (9 requested) atoms. Cycle 9: After refmac, R = 0.2021 (Rfree = 0.000) for 2446 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.1986 (Rfree = 0.000) for 2437 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 3.17 Search for helices and strands: 0 residues in 0 chains, 2512 seeds are put forward Round 1: 189 peptides, 32 chains. Longest chain 14 peptides. Score 0.451 Round 2: 206 peptides, 25 chains. Longest chain 20 peptides. Score 0.623 Round 3: 195 peptides, 25 chains. Longest chain 23 peptides. Score 0.588 Round 4: 211 peptides, 25 chains. Longest chain 28 peptides. Score 0.638 Round 5: 212 peptides, 26 chains. Longest chain 23 peptides. Score 0.628 Taking the results from Round 4 Chains 26, Residues 186, Estimated correctness of the model 40.6 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5372 reflections ( 99.76 % complete ) and 5298 restraints for refining 2480 atoms. 4527 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2243 (Rfree = 0.000) for 2480 atoms. Found 9 (18 requested) and removed 9 (9 requested) atoms. Cycle 12: After refmac, R = 0.2085 (Rfree = 0.000) for 2466 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 13: After refmac, R = 0.1999 (Rfree = 0.000) for 2457 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.1961 (Rfree = 0.000) for 2450 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. Cycle 15: After refmac, R = 0.1937 (Rfree = 0.000) for 2441 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 3.18 Search for helices and strands: 0 residues in 0 chains, 2521 seeds are put forward Round 1: 181 peptides, 29 chains. Longest chain 24 peptides. Score 0.471 Round 2: 191 peptides, 25 chains. Longest chain 26 peptides. Score 0.574 Round 3: 204 peptides, 26 chains. Longest chain 21 peptides. Score 0.602 Round 4: 205 peptides, 25 chains. Longest chain 28 peptides. Score 0.620 Round 5: 204 peptides, 27 chains. Longest chain 19 peptides. Score 0.588 Taking the results from Round 4 Chains 25, Residues 180, Estimated correctness of the model 35.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5372 reflections ( 99.76 % complete ) and 5531 restraints for refining 2480 atoms. 4836 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2158 (Rfree = 0.000) for 2480 atoms. Found 12 (18 requested) and removed 10 (9 requested) atoms. Cycle 17: After refmac, R = 0.2036 (Rfree = 0.000) for 2477 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. Cycle 18: After refmac, R = 0.1996 (Rfree = 0.000) for 2469 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.1956 (Rfree = 0.000) for 2464 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.1938 (Rfree = 0.000) for 2456 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.19 Search for helices and strands: 0 residues in 0 chains, 2531 seeds are put forward Round 1: 181 peptides, 28 chains. Longest chain 14 peptides. Score 0.488 Round 2: 185 peptides, 23 chains. Longest chain 17 peptides. Score 0.584 Round 3: 171 peptides, 19 chains. Longest chain 20 peptides. Score 0.599 Round 4: 193 peptides, 21 chains. Longest chain 23 peptides. Score 0.640 Round 5: 180 peptides, 23 chains. Longest chain 19 peptides. Score 0.567 Taking the results from Round 4 Chains 21, Residues 172, Estimated correctness of the model 41.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5372 reflections ( 99.76 % complete ) and 5693 restraints for refining 2481 atoms. 5026 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2173 (Rfree = 0.000) for 2481 atoms. Found 11 (18 requested) and removed 9 (9 requested) atoms. Cycle 22: After refmac, R = 0.2074 (Rfree = 0.000) for 2481 atoms. Found 5 (18 requested) and removed 10 (9 requested) atoms. Cycle 23: After refmac, R = 0.2040 (Rfree = 0.000) for 2473 atoms. Found 8 (18 requested) and removed 9 (9 requested) atoms. Cycle 24: After refmac, R = 0.1999 (Rfree = 0.000) for 2472 atoms. Found 5 (18 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.1973 (Rfree = 0.000) for 2468 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 3.18 Search for helices and strands: 0 residues in 0 chains, 2521 seeds are put forward Round 1: 191 peptides, 30 chains. Longest chain 14 peptides. Score 0.493 Round 2: 204 peptides, 26 chains. Longest chain 19 peptides. Score 0.602 Round 3: 206 peptides, 24 chains. Longest chain 31 peptides. Score 0.637 Round 4: 202 peptides, 25 chains. Longest chain 26 peptides. Score 0.611 Round 5: 203 peptides, 28 chains. Longest chain 20 peptides. Score 0.569 Taking the results from Round 3 Chains 24, Residues 182, Estimated correctness of the model 40.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5372 reflections ( 99.76 % complete ) and 5624 restraints for refining 2481 atoms. 4920 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2146 (Rfree = 0.000) for 2481 atoms. Found 11 (18 requested) and removed 10 (9 requested) atoms. Cycle 27: After refmac, R = 0.2037 (Rfree = 0.000) for 2479 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. Cycle 28: After refmac, R = 0.1984 (Rfree = 0.000) for 2476 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.1975 (Rfree = 0.000) for 2468 atoms. Found 4 (18 requested) and removed 10 (9 requested) atoms. Cycle 30: After refmac, R = 0.1949 (Rfree = 0.000) for 2460 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 3.20 Search for helices and strands: 0 residues in 0 chains, 2520 seeds are put forward Round 1: 185 peptides, 30 chains. Longest chain 14 peptides. Score 0.470 Round 2: 200 peptides, 24 chains. Longest chain 22 peptides. Score 0.619 Round 3: 214 peptides, 27 chains. Longest chain 18 peptides. Score 0.620 Round 4: 206 peptides, 26 chains. Longest chain 26 peptides. Score 0.609 Round 5: 194 peptides, 25 chains. Longest chain 18 peptides. Score 0.584 Taking the results from Round 3 Chains 27, Residues 187, Estimated correctness of the model 35.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5372 reflections ( 99.76 % complete ) and 5550 restraints for refining 2481 atoms. 4829 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2186 (Rfree = 0.000) for 2481 atoms. Found 9 (18 requested) and removed 10 (9 requested) atoms. Cycle 32: After refmac, R = 0.2011 (Rfree = 0.000) for 2477 atoms. Found 5 (18 requested) and removed 10 (9 requested) atoms. Cycle 33: After refmac, R = 0.1980 (Rfree = 0.000) for 2470 atoms. Found 4 (18 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.1961 (Rfree = 0.000) for 2464 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.1946 (Rfree = 0.000) for 2458 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 3.19 Search for helices and strands: 0 residues in 0 chains, 2528 seeds are put forward Round 1: 179 peptides, 29 chains. Longest chain 14 peptides. Score 0.463 Round 2: 193 peptides, 27 chains. Longest chain 19 peptides. Score 0.550 Round 3: 180 peptides, 21 chains. Longest chain 20 peptides. Score 0.598 Round 4: 184 peptides, 24 chains. Longest chain 19 peptides. Score 0.565 Round 5: 197 peptides, 25 chains. Longest chain 18 peptides. Score 0.594 Taking the results from Round 3 Chains 21, Residues 159, Estimated correctness of the model 28.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5372 reflections ( 99.76 % complete ) and 5666 restraints for refining 2481 atoms. 5051 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2050 (Rfree = 0.000) for 2481 atoms. Found 9 (18 requested) and removed 9 (9 requested) atoms. Cycle 37: After refmac, R = 0.1925 (Rfree = 0.000) for 2477 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 38: After refmac, R = 0.1888 (Rfree = 0.000) for 2469 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.1903 (Rfree = 0.000) for 2462 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.1853 (Rfree = 0.000) for 2455 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 3.18 Search for helices and strands: 0 residues in 0 chains, 2538 seeds are put forward Round 1: 153 peptides, 25 chains. Longest chain 12 peptides. Score 0.427 Round 2: 168 peptides, 23 chains. Longest chain 16 peptides. Score 0.523 Round 3: 172 peptides, 23 chains. Longest chain 16 peptides. Score 0.538 Round 4: 181 peptides, 22 chains. Longest chain 33 peptides. Score 0.586 Round 5: 182 peptides, 24 chains. Longest chain 16 peptides. Score 0.558 Taking the results from Round 4 Chains 22, Residues 159, Estimated correctness of the model 24.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5372 reflections ( 99.76 % complete ) and 5623 restraints for refining 2481 atoms. 5009 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2098 (Rfree = 0.000) for 2481 atoms. Found 10 (18 requested) and removed 9 (9 requested) atoms. Cycle 42: After refmac, R = 0.1997 (Rfree = 0.000) for 2480 atoms. Found 9 (18 requested) and removed 9 (9 requested) atoms. Cycle 43: After refmac, R = 0.1984 (Rfree = 0.000) for 2480 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 44: After refmac, R = 0.1946 (Rfree = 0.000) for 2469 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.1934 (Rfree = 0.000) for 2463 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.19 Search for helices and strands: 0 residues in 0 chains, 2534 seeds are put forward Round 1: 144 peptides, 25 chains. Longest chain 13 peptides. Score 0.387 Round 2: 163 peptides, 24 chains. Longest chain 16 peptides. Score 0.486 Round 3: 172 peptides, 23 chains. Longest chain 19 peptides. Score 0.538 Round 4: 169 peptides, 26 chains. Longest chain 18 peptides. Score 0.475 Round 5: 153 peptides, 21 chains. Longest chain 16 peptides. Score 0.500 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 149, Estimated correctness of the model 7.2 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vqz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5372 reflections ( 99.76 % complete ) and 5674 restraints for refining 2480 atoms. 5101 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2079 (Rfree = 0.000) for 2480 atoms. Found 0 (18 requested) and removed 8 (9 requested) atoms. Cycle 47: After refmac, R = 0.2029 (Rfree = 0.000) for 2470 atoms. Found 0 (18 requested) and removed 2 (9 requested) atoms. Cycle 48: After refmac, R = 0.2075 (Rfree = 0.000) for 2468 atoms. Found 0 (18 requested) and removed 2 (9 requested) atoms. Cycle 49: After refmac, R = 0.2103 (Rfree = 0.000) for 2466 atoms. TimeTaking 46.98