Sun 23 Dec 22:22:43 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 1vk4-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk4-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk4-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-4.0-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/1vk4-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-4.0-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 22:22:53 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/1vk4-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-4.0-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 185 and 0 Target number of residues in the AU: 185 Target solvent content: 0.6489 Checking the provided sequence file Detected sequence length: 298 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 298 Adjusted target solvent content: 0.43 Input MTZ file: 1vk4-4.0-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: 43.308 68.545 96.054 90.000 90.000 90.000 Input sequence file: 1vk4-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2384 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: 55.795 4.000 Wilson plot Bfac: 76.57 2626 reflections ( 98.80 % complete ) and 0 restraints for refining 2632 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3147 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3019 (Rfree = 0.000) for 2632 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 4.02 Search for helices and strands: 0 residues in 0 chains, 2686 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 10 peptides. Score 0.248 Round 2: 135 peptides, 24 chains. Longest chain 13 peptides. Score 0.406 Round 3: 149 peptides, 22 chains. Longest chain 14 peptides. Score 0.522 Round 4: 165 peptides, 23 chains. Longest chain 15 peptides. Score 0.575 Round 5: 166 peptides, 24 chains. Longest chain 15 peptides. Score 0.560 Taking the results from Round 4 Chains 23, Residues 142, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 2626 reflections ( 98.80 % complete ) and 4688 restraints for refining 2124 atoms. 4063 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2432 (Rfree = 0.000) for 2124 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 2: After refmac, R = 0.2276 (Rfree = 0.000) for 2065 atoms. Found 8 (10 requested) and removed 8 (5 requested) atoms. Cycle 3: After refmac, R = 0.2200 (Rfree = 0.000) for 2050 atoms. Found 1 (9 requested) and removed 8 (4 requested) atoms. Cycle 4: After refmac, R = 0.2151 (Rfree = 0.000) for 2035 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2138 (Rfree = 0.000) for 2029 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 2104 seeds are put forward Round 1: 117 peptides, 22 chains. Longest chain 10 peptides. Score 0.352 Round 2: 151 peptides, 21 chains. Longest chain 18 peptides. Score 0.552 Round 3: 154 peptides, 21 chains. Longest chain 18 peptides. Score 0.565 Round 4: 148 peptides, 21 chains. Longest chain 13 peptides. Score 0.538 Round 5: 150 peptides, 18 chains. Longest chain 15 peptides. Score 0.606 Taking the results from Round 5 Chains 18, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2626 reflections ( 98.80 % complete ) and 5007 restraints for refining 2110 atoms. 4497 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2278 (Rfree = 0.000) for 2110 atoms. Found 7 (10 requested) and removed 10 (5 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.1975 (Rfree = 0.000) for 2081 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 8: After refmac, R = 0.1912 (Rfree = 0.000) for 2066 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.1833 (Rfree = 0.000) for 2057 atoms. Found 2 (9 requested) and removed 8 (4 requested) atoms. Cycle 10: After refmac, R = 0.1767 (Rfree = 0.000) for 2049 atoms. Found 4 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 2122 seeds are put forward Round 1: 123 peptides, 24 chains. Longest chain 11 peptides. Score 0.337 Round 2: 137 peptides, 20 chains. Longest chain 18 peptides. Score 0.506 Round 3: 143 peptides, 17 chains. Longest chain 32 peptides. Score 0.596 Round 4: 148 peptides, 19 chains. Longest chain 21 peptides. Score 0.578 Round 5: 150 peptides, 19 chains. Longest chain 27 peptides. Score 0.587 Taking the results from Round 3 Chains 17, Residues 126, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2626 reflections ( 98.80 % complete ) and 4673 restraints for refining 2067 atoms. 4167 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2047 (Rfree = 0.000) for 2067 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 12: After refmac, R = 0.1720 (Rfree = 0.000) for 2041 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 13: After refmac, R = 0.1617 (Rfree = 0.000) for 2036 atoms. Found 0 (9 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.1498 (Rfree = 0.000) for 2027 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.1476 (Rfree = 0.000) for 2024 atoms. Found 0 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.94 Search for helices and strands: 0 residues in 0 chains, 2091 seeds are put forward Round 1: 128 peptides, 26 chains. Longest chain 12 peptides. Score 0.317 Round 2: 142 peptides, 22 chains. Longest chain 17 peptides. Score 0.488 Round 3: 136 peptides, 19 chains. Longest chain 21 peptides. Score 0.523 Round 4: 145 peptides, 20 chains. Longest chain 19 peptides. Score 0.544 Round 5: 140 peptides, 23 chains. Longest chain 10 peptides. Score 0.455 Taking the results from Round 4 Chains 20, Residues 125, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 2626 reflections ( 98.80 % complete ) and 4814 restraints for refining 2153 atoms. 4273 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2160 (Rfree = 0.000) for 2153 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 17: After refmac, R = 0.1984 (Rfree = 0.000) for 2125 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.1889 (Rfree = 0.000) for 2109 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.1841 (Rfree = 0.000) for 2095 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.1777 (Rfree = 0.000) for 2088 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.86 Search for helices and strands: 0 residues in 0 chains, 2166 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 7 peptides. Score 0.243 Round 2: 118 peptides, 21 chains. Longest chain 13 peptides. Score 0.382 Round 3: 144 peptides, 26 chains. Longest chain 14 peptides. Score 0.408 Round 4: 139 peptides, 25 chains. Longest chain 15 peptides. Score 0.404 Round 5: 129 peptides, 21 chains. Longest chain 13 peptides. Score 0.443 Taking the results from Round 5 Chains 21, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2626 reflections ( 98.80 % complete ) and 5132 restraints for refining 2153 atoms. 4721 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2072 (Rfree = 0.000) for 2153 atoms. Found 9 (10 requested) and removed 120 (5 requested) atoms. Cycle 22: After refmac, R = 0.1812 (Rfree = 0.000) for 2020 atoms. Found 5 (9 requested) and removed 33 (4 requested) atoms. Cycle 23: After refmac, R = 0.1587 (Rfree = 0.000) for 1983 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 24: After refmac, R = 0.1451 (Rfree = 0.000) for 1973 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.1563 (Rfree = 0.000) for 1966 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.98 Search for helices and strands: 0 residues in 0 chains, 2027 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 7 peptides. Score 0.249 Round 2: 128 peptides, 23 chains. Longest chain 16 peptides. Score 0.390 Round 3: 125 peptides, 21 chains. Longest chain 15 peptides. Score 0.421 Round 4: 119 peptides, 18 chains. Longest chain 13 peptides. Score 0.460 Round 5: 116 peptides, 17 chains. Longest chain 15 peptides. Score 0.467 Taking the results from Round 5 Chains 17, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2626 reflections ( 98.80 % complete ) and 4842 restraints for refining 2085 atoms. 4463 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1939 (Rfree = 0.000) for 2085 atoms. Found 8 (9 requested) and removed 14 (4 requested) atoms. Cycle 27: After refmac, R = 0.1584 (Rfree = 0.000) for 2075 atoms. Found 8 (9 requested) and removed 11 (4 requested) atoms. Cycle 28: After refmac, R = 0.1634 (Rfree = 0.000) for 2069 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.1437 (Rfree = 0.000) for 2063 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.1394 (Rfree = 0.000) for 2060 atoms. Found 3 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 3.97 Search for helices and strands: 0 residues in 0 chains, 2103 seeds are put forward Round 1: 91 peptides, 20 chains. Longest chain 7 peptides. Score 0.242 Round 2: 112 peptides, 20 chains. Longest chain 12 peptides. Score 0.372 Round 3: 123 peptides, 22 chains. Longest chain 13 peptides. Score 0.386 Round 4: 129 peptides, 22 chains. Longest chain 15 peptides. Score 0.420 Round 5: 132 peptides, 20 chains. Longest chain 15 peptides. Score 0.481 Taking the results from Round 5 Chains 20, Residues 112, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2626 reflections ( 98.80 % complete ) and 5060 restraints for refining 2153 atoms. 4614 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1720 (Rfree = 0.000) for 2153 atoms. Found 4 (10 requested) and removed 31 (5 requested) atoms. Cycle 32: After refmac, R = 0.1534 (Rfree = 0.000) for 2121 atoms. Found 4 (10 requested) and removed 11 (5 requested) atoms. Cycle 33: After refmac, R = 0.1581 (Rfree = 0.000) for 2111 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. Cycle 34: After refmac, R = 0.1504 (Rfree = 0.000) for 2106 atoms. Found 7 (10 requested) and removed 9 (5 requested) atoms. Cycle 35: After refmac, R = 0.1320 (Rfree = 0.000) for 2101 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 4.01 Search for helices and strands: 0 residues in 0 chains, 2165 seeds are put forward Round 1: 98 peptides, 22 chains. Longest chain 6 peptides. Score 0.234 Round 2: 113 peptides, 22 chains. Longest chain 13 peptides. Score 0.328 Round 3: 117 peptides, 22 chains. Longest chain 11 peptides. Score 0.352 Round 4: 118 peptides, 20 chains. Longest chain 13 peptides. Score 0.406 Round 5: 118 peptides, 22 chains. Longest chain 10 peptides. Score 0.357 Taking the results from Round 4 Chains 20, Residues 98, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2626 reflections ( 98.80 % complete ) and 4986 restraints for refining 2149 atoms. 4595 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1593 (Rfree = 0.000) for 2149 atoms. Found 8 (10 requested) and removed 118 (5 requested) atoms. Cycle 37: After refmac, R = 0.1705 (Rfree = 0.000) for 2037 atoms. Found 5 (9 requested) and removed 12 (4 requested) atoms. Cycle 38: After refmac, R = 0.1353 (Rfree = 0.000) for 2025 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.1287 (Rfree = 0.000) for 2020 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1224 (Rfree = 0.000) for 2016 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 3.98 Search for helices and strands: 0 residues in 0 chains, 2068 seeds are put forward Round 1: 89 peptides, 21 chains. Longest chain 6 peptides. Score 0.201 Round 2: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.296 Round 3: 92 peptides, 18 chains. Longest chain 7 peptides. Score 0.303 Round 4: 98 peptides, 19 chains. Longest chain 11 peptides. Score 0.314 Round 5: 103 peptides, 20 chains. Longest chain 7 peptides. Score 0.319 Taking the results from Round 5 Chains 20, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2626 reflections ( 98.80 % complete ) and 5227 restraints for refining 2146 atoms. 4915 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1525 (Rfree = 0.000) for 2146 atoms. Found 5 (10 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.1425 (Rfree = 0.000) for 2131 atoms. Found 9 (10 requested) and removed 13 (5 requested) atoms. Cycle 43: After refmac, R = 0.1379 (Rfree = 0.000) for 2124 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.1214 (Rfree = 0.000) for 2119 atoms. Found 0 (10 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.1233 (Rfree = 0.000) for 2113 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.94 Search for helices and strands: 0 residues in 0 chains, 2170 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.238 Round 2: 90 peptides, 16 chains. Longest chain 12 peptides. Score 0.344 Round 3: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.313 Round 4: 93 peptides, 17 chains. Longest chain 12 peptides. Score 0.336 Round 5: 90 peptides, 18 chains. Longest chain 7 peptides. Score 0.290 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 74, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 1vk4-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2626 reflections ( 98.80 % complete ) and 5115 restraints for refining 2153 atoms. 4803 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1428 (Rfree = 0.000) for 2153 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1733 (Rfree = 0.000) for 2140 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2163 (Rfree = 0.000) for 2129 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1471 (Rfree = 0.000) for 2118 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 33.45