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 2hxv-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hxv-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hxv-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-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/2hxv-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-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 22:22:53 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/2hxv-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-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 257 and 0 Target number of residues in the AU: 257 Target solvent content: 0.6509 Checking the provided sequence file Detected sequence length: 360 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 360 Adjusted target solvent content: 0.51 Input MTZ file: 2hxv-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: 97 Cell parameters: 104.410 104.410 146.200 90.000 90.000 90.000 Input sequence file: 2hxv-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2880 target number of atoms Had to go as low as 0.65 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: 84.967 3.800 Wilson plot Bfac: 78.09 4227 reflections ( 99.34 % complete ) and 0 restraints for refining 3192 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3444 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3344 (Rfree = 0.000) for 3192 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.59 Search for helices and strands: 0 residues in 0 chains, 3232 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 6 peptides. Score 0.225 Round 2: 151 peptides, 27 chains. Longest chain 10 peptides. Score 0.366 Round 3: 180 peptides, 28 chains. Longest chain 18 peptides. Score 0.464 Round 4: 201 peptides, 28 chains. Longest chain 21 peptides. Score 0.538 Round 5: 196 peptides, 27 chains. Longest chain 24 peptides. Score 0.536 Taking the results from Round 4 Chains 30, Residues 173, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4227 reflections ( 99.34 % complete ) and 5758 restraints for refining 2596 atoms. 5013 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2844 (Rfree = 0.000) for 2596 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 2: After refmac, R = 0.2733 (Rfree = 0.000) for 2543 atoms. Found 8 (14 requested) and removed 17 (7 requested) atoms. Cycle 3: After refmac, R = 0.2528 (Rfree = 0.000) for 2518 atoms. Found 9 (13 requested) and removed 12 (6 requested) atoms. Cycle 4: After refmac, R = 0.2396 (Rfree = 0.000) for 2506 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2241 (Rfree = 0.000) for 2499 atoms. Found 0 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.56 Search for helices and strands: 0 residues in 0 chains, 2569 seeds are put forward Round 1: 179 peptides, 32 chains. Longest chain 12 peptides. Score 0.393 Round 2: 205 peptides, 32 chains. Longest chain 14 peptides. Score 0.491 Round 3: 197 peptides, 29 chains. Longest chain 25 peptides. Score 0.509 Round 4: 196 peptides, 26 chains. Longest chain 24 peptides. Score 0.551 Round 5: 202 peptides, 25 chains. Longest chain 22 peptides. Score 0.584 Taking the results from Round 5 Chains 25, Residues 177, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4227 reflections ( 99.34 % complete ) and 5988 restraints for refining 2605 atoms. 5277 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2476 (Rfree = 0.000) for 2605 atoms. Found 7 (14 requested) and removed 22 (7 requested) atoms. Cycle 7: After refmac, R = 0.2273 (Rfree = 0.000) for 2570 atoms. Found 4 (14 requested) and removed 19 (7 requested) atoms. Cycle 8: After refmac, R = 0.2050 (Rfree = 0.000) for 2537 atoms. Found 4 (14 requested) and removed 15 (7 requested) atoms. Cycle 9: After refmac, R = 0.2149 (Rfree = 0.000) for 2517 atoms. Found 7 (13 requested) and removed 12 (6 requested) atoms. Cycle 10: After refmac, R = 0.1946 (Rfree = 0.000) for 2508 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.54 Search for helices and strands: 0 residues in 0 chains, 2575 seeds are put forward Round 1: 155 peptides, 26 chains. Longest chain 13 peptides. Score 0.400 Round 2: 186 peptides, 32 chains. Longest chain 13 peptides. Score 0.421 Round 3: 196 peptides, 31 chains. Longest chain 15 peptides. Score 0.474 Round 4: 188 peptides, 25 chains. Longest chain 22 peptides. Score 0.539 Round 5: 179 peptides, 26 chains. Longest chain 15 peptides. Score 0.492 Taking the results from Round 4 Chains 25, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4227 reflections ( 99.34 % complete ) and 6011 restraints for refining 2598 atoms. 5384 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2271 (Rfree = 0.000) for 2598 atoms. Found 11 (14 requested) and removed 89 (7 requested) atoms. Cycle 12: After refmac, R = 0.2179 (Rfree = 0.000) for 2508 atoms. Found 9 (13 requested) and removed 41 (6 requested) atoms. Cycle 13: After refmac, R = 0.2220 (Rfree = 0.000) for 2468 atoms. Found 5 (13 requested) and removed 21 (6 requested) atoms. Cycle 14: After refmac, R = 0.2104 (Rfree = 0.000) for 2437 atoms. Found 5 (13 requested) and removed 19 (6 requested) atoms. Cycle 15: After refmac, R = 0.1864 (Rfree = 0.000) for 2415 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.54 Search for helices and strands: 0 residues in 0 chains, 2483 seeds are put forward Round 1: 167 peptides, 33 chains. Longest chain 9 peptides. Score 0.326 Round 2: 189 peptides, 31 chains. Longest chain 14 peptides. Score 0.448 Round 3: 200 peptides, 33 chains. Longest chain 12 peptides. Score 0.457 Round 4: 196 peptides, 28 chains. Longest chain 18 peptides. Score 0.521 Round 5: 209 peptides, 31 chains. Longest chain 15 peptides. Score 0.520 Taking the results from Round 4 Chains 29, Residues 168, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4227 reflections ( 99.34 % complete ) and 5638 restraints for refining 2582 atoms. 4932 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2305 (Rfree = 0.000) for 2582 atoms. Found 8 (14 requested) and removed 39 (7 requested) atoms. Cycle 17: After refmac, R = 0.2226 (Rfree = 0.000) for 2528 atoms. Found 6 (14 requested) and removed 22 (7 requested) atoms. Cycle 18: After refmac, R = 0.2114 (Rfree = 0.000) for 2502 atoms. Found 1 (13 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.2068 (Rfree = 0.000) for 2491 atoms. Found 4 (13 requested) and removed 13 (6 requested) atoms. Cycle 20: After refmac, R = 0.1854 (Rfree = 0.000) for 2476 atoms. Found 0 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 2519 seeds are put forward Round 1: 164 peptides, 32 chains. Longest chain 10 peptides. Score 0.331 Round 2: 186 peptides, 29 chains. Longest chain 15 peptides. Score 0.470 Round 3: 178 peptides, 28 chains. Longest chain 12 peptides. Score 0.456 Round 4: 180 peptides, 26 chains. Longest chain 15 peptides. Score 0.496 Round 5: 185 peptides, 28 chains. Longest chain 15 peptides. Score 0.482 Taking the results from Round 4 Chains 27, Residues 154, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4227 reflections ( 99.34 % complete ) and 5972 restraints for refining 2605 atoms. 5353 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2173 (Rfree = 0.000) for 2605 atoms. Found 7 (14 requested) and removed 33 (7 requested) atoms. Cycle 22: After refmac, R = 0.2072 (Rfree = 0.000) for 2569 atoms. Found 4 (14 requested) and removed 13 (7 requested) atoms. Cycle 23: After refmac, R = 0.2060 (Rfree = 0.000) for 2553 atoms. Found 2 (14 requested) and removed 17 (7 requested) atoms. Cycle 24: After refmac, R = 0.2062 (Rfree = 0.000) for 2534 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.1868 (Rfree = 0.000) for 2527 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 2573 seeds are put forward Round 1: 129 peptides, 25 chains. Longest chain 11 peptides. Score 0.308 Round 2: 163 peptides, 27 chains. Longest chain 12 peptides. Score 0.415 Round 3: 169 peptides, 28 chains. Longest chain 9 peptides. Score 0.422 Round 4: 168 peptides, 25 chains. Longest chain 14 peptides. Score 0.468 Round 5: 160 peptides, 21 chains. Longest chain 23 peptides. Score 0.505 Taking the results from Round 5 Chains 23, Residues 139, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4227 reflections ( 99.34 % complete ) and 5940 restraints for refining 2605 atoms. 5362 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2180 (Rfree = 0.000) for 2605 atoms. Found 7 (14 requested) and removed 21 (7 requested) atoms. Cycle 27: After refmac, R = 0.1965 (Rfree = 0.000) for 2572 atoms. Found 3 (14 requested) and removed 11 (7 requested) atoms. Cycle 28: After refmac, R = 0.1913 (Rfree = 0.000) for 2558 atoms. Found 1 (14 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.1883 (Rfree = 0.000) for 2547 atoms. Found 2 (14 requested) and removed 14 (7 requested) atoms. Cycle 30: After refmac, R = 0.1872 (Rfree = 0.000) for 2528 atoms. Found 0 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.13 4.08 Search for helices and strands: 0 residues in 0 chains, 2566 seeds are put forward Round 1: 126 peptides, 26 chains. Longest chain 9 peptides. Score 0.274 Round 2: 143 peptides, 26 chains. Longest chain 15 peptides. Score 0.350 Round 3: 153 peptides, 24 chains. Longest chain 18 peptides. Score 0.427 Round 4: 146 peptides, 23 chains. Longest chain 16 peptides. Score 0.417 Round 5: 153 peptides, 24 chains. Longest chain 15 peptides. Score 0.427 Taking the results from Round 5 Chains 25, Residues 129, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4227 reflections ( 99.34 % complete ) and 5994 restraints for refining 2605 atoms. 5459 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2127 (Rfree = 0.000) for 2605 atoms. Found 3 (14 requested) and removed 19 (7 requested) atoms. Cycle 32: After refmac, R = 0.1976 (Rfree = 0.000) for 2574 atoms. Found 2 (14 requested) and removed 11 (7 requested) atoms. Cycle 33: After refmac, R = 0.1934 (Rfree = 0.000) for 2559 atoms. Found 0 (14 requested) and removed 8 (7 requested) atoms. Cycle 34: After refmac, R = 0.1900 (Rfree = 0.000) for 2547 atoms. Found 6 (14 requested) and removed 12 (7 requested) atoms. Cycle 35: After refmac, R = 0.1873 (Rfree = 0.000) for 2538 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.55 Search for helices and strands: 0 residues in 0 chains, 2599 seeds are put forward Round 1: 125 peptides, 27 chains. Longest chain 9 peptides. Score 0.250 Round 2: 152 peptides, 28 chains. Longest chain 10 peptides. Score 0.352 Round 3: 149 peptides, 25 chains. Longest chain 12 peptides. Score 0.394 Round 4: 163 peptides, 28 chains. Longest chain 13 peptides. Score 0.398 Round 5: 148 peptides, 23 chains. Longest chain 13 peptides. Score 0.425 Taking the results from Round 5 Chains 23, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4227 reflections ( 99.34 % complete ) and 6235 restraints for refining 2605 atoms. 5758 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2308 (Rfree = 0.000) for 2605 atoms. Found 9 (14 requested) and removed 16 (7 requested) atoms. Cycle 37: After refmac, R = 0.2017 (Rfree = 0.000) for 2584 atoms. Found 5 (14 requested) and removed 10 (7 requested) atoms. Cycle 38: After refmac, R = 0.1845 (Rfree = 0.000) for 2574 atoms. Found 1 (14 requested) and removed 9 (7 requested) atoms. Cycle 39: After refmac, R = 0.1838 (Rfree = 0.000) for 2565 atoms. Found 1 (14 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1785 (Rfree = 0.000) for 2556 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.61 Search for helices and strands: 0 residues in 0 chains, 2607 seeds are put forward Round 1: 155 peptides, 33 chains. Longest chain 9 peptides. Score 0.274 Round 2: 161 peptides, 27 chains. Longest chain 11 peptides. Score 0.407 Round 3: 153 peptides, 27 chains. Longest chain 11 peptides. Score 0.374 Round 4: 157 peptides, 25 chains. Longest chain 13 peptides. Score 0.426 Round 5: 142 peptides, 24 chains. Longest chain 9 peptides. Score 0.383 Taking the results from Round 4 Chains 25, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4227 reflections ( 99.34 % complete ) and 6132 restraints for refining 2604 atoms. 5629 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2306 (Rfree = 0.000) for 2604 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. Cycle 42: After refmac, R = 0.2053 (Rfree = 0.000) for 2599 atoms. Found 0 (14 requested) and removed 12 (7 requested) atoms. Cycle 43: After refmac, R = 0.1971 (Rfree = 0.000) for 2581 atoms. Found 0 (14 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.1945 (Rfree = 0.000) for 2569 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.2062 (Rfree = 0.000) for 2557 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 3.58 Search for helices and strands: 0 residues in 0 chains, 2611 seeds are put forward Round 1: 105 peptides, 24 chains. Longest chain 6 peptides. Score 0.213 Round 2: 132 peptides, 26 chains. Longest chain 10 peptides. Score 0.302 Round 3: 126 peptides, 20 chains. Longest chain 18 peptides. Score 0.389 Round 4: 126 peptides, 24 chains. Longest chain 11 peptides. Score 0.313 Round 5: 125 peptides, 22 chains. Longest chain 15 peptides. Score 0.347 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 106, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2hxv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4227 reflections ( 99.34 % complete ) and 6303 restraints for refining 2605 atoms. 5868 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2131 (Rfree = 0.000) for 2605 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1952 (Rfree = 0.000) for 2593 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1904 (Rfree = 0.000) for 2585 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1874 (Rfree = 0.000) for 2575 atoms. TimeTaking 50.48