Sun 23 Dec 22:22:49 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 1vpm-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpm-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpm-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-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/1vpm-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-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 22:22:58 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/1vpm-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-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 327 and 0 Target number of residues in the AU: 327 Target solvent content: 0.6665 Checking the provided sequence file Detected sequence length: 169 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 507 Adjusted target solvent content: 0.48 Input MTZ file: 1vpm-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: 24 Cell parameters: 82.941 106.484 120.177 90.000 90.000 90.000 Input sequence file: 1vpm-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 4056 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 79.699 4.001 Wilson plot Bfac: 89.10 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4611 reflections ( 97.44 % complete ) and 0 restraints for refining 4479 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3190 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3454 (Rfree = 0.000) for 4479 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.78 3.88 Search for helices and strands: 0 residues in 0 chains, 4569 seeds are put forward NCS extension: 0 residues added, 4569 seeds are put forward Round 1: 199 peptides, 41 chains. Longest chain 9 peptides. Score 0.290 Round 2: 262 peptides, 37 chains. Longest chain 18 peptides. Score 0.527 Round 3: 264 peptides, 34 chains. Longest chain 16 peptides. Score 0.565 Round 4: 271 peptides, 34 chains. Longest chain 23 peptides. Score 0.582 Round 5: 274 peptides, 30 chains. Longest chain 29 peptides. Score 0.629 Taking the results from Round 5 Chains 30, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8568 restraints for refining 3660 atoms. 7622 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2662 (Rfree = 0.000) for 3660 atoms. Found 14 (17 requested) and removed 32 (8 requested) atoms. Cycle 2: After refmac, R = 0.2504 (Rfree = 0.000) for 3569 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 3: After refmac, R = 0.2514 (Rfree = 0.000) for 3512 atoms. Found 16 (16 requested) and removed 74 (8 requested) atoms. Cycle 4: After refmac, R = 0.1967 (Rfree = 0.000) for 3412 atoms. Found 8 (16 requested) and removed 44 (8 requested) atoms. Cycle 5: After refmac, R = 0.1898 (Rfree = 0.000) for 3360 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.81 3.91 Search for helices and strands: 0 residues in 0 chains, 3481 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3505 seeds are put forward Round 1: 223 peptides, 42 chains. Longest chain 15 peptides. Score 0.354 Round 2: 245 peptides, 39 chains. Longest chain 17 peptides. Score 0.458 Round 3: 258 peptides, 37 chains. Longest chain 19 peptides. Score 0.516 Round 4: 246 peptides, 37 chains. Longest chain 15 peptides. Score 0.485 Round 5: 248 peptides, 31 chains. Longest chain 25 peptides. Score 0.559 Taking the results from Round 5 Chains 31, Residues 217, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8420 restraints for refining 3530 atoms. 7583 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2629 (Rfree = 0.000) for 3530 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 7: After refmac, R = 0.2247 (Rfree = 0.000) for 3473 atoms. Found 16 (16 requested) and removed 38 (8 requested) atoms. Cycle 8: After refmac, R = 0.2370 (Rfree = 0.000) for 3422 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 9: After refmac, R = 0.2171 (Rfree = 0.000) for 3391 atoms. Found 13 (16 requested) and removed 17 (8 requested) atoms. Cycle 10: After refmac, R = 0.2055 (Rfree = 0.000) for 3366 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 3524 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3544 seeds are put forward Round 1: 223 peptides, 42 chains. Longest chain 12 peptides. Score 0.354 Round 2: 235 peptides, 35 chains. Longest chain 17 peptides. Score 0.478 Round 3: 241 peptides, 35 chains. Longest chain 21 peptides. Score 0.495 Round 4: 230 peptides, 31 chains. Longest chain 20 peptides. Score 0.513 Round 5: 257 peptides, 30 chains. Longest chain 28 peptides. Score 0.592 Taking the results from Round 5 Chains 32, Residues 227, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 7774 restraints for refining 3514 atoms. 6828 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2145 (Rfree = 0.000) for 3514 atoms. Found 16 (16 requested) and removed 50 (8 requested) atoms. Cycle 12: After refmac, R = 0.2058 (Rfree = 0.000) for 3449 atoms. Found 16 (16 requested) and removed 31 (8 requested) atoms. Cycle 13: After refmac, R = 0.1907 (Rfree = 0.000) for 3418 atoms. Found 16 (16 requested) and removed 40 (8 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1770 (Rfree = 0.000) for 3383 atoms. Found 14 (16 requested) and removed 117 (8 requested) atoms. Cycle 15: After refmac, R = 0.1931 (Rfree = 0.000) for 3269 atoms. Found 15 (15 requested) and removed 33 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 3399 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 3429 seeds are put forward Round 1: 213 peptides, 39 chains. Longest chain 18 peptides. Score 0.362 Round 2: 248 peptides, 38 chains. Longest chain 12 peptides. Score 0.478 Round 3: 233 peptides, 33 chains. Longest chain 19 peptides. Score 0.497 Round 4: 240 peptides, 34 chains. Longest chain 17 peptides. Score 0.504 Round 5: 231 peptides, 32 chains. Longest chain 16 peptides. Score 0.504 Taking the results from Round 5 Chains 35, Residues 199, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 7637 restraints for refining 3423 atoms. 6818 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2156 (Rfree = 0.000) for 3423 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 17: After refmac, R = 0.2125 (Rfree = 0.000) for 3381 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 18: After refmac, R = 0.1938 (Rfree = 0.000) for 3356 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 19: After refmac, R = 0.1900 (Rfree = 0.000) for 3350 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 20: After refmac, R = 0.1970 (Rfree = 0.000) for 3346 atoms. Found 15 (15 requested) and removed 55 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.79 3.89 Search for helices and strands: 0 residues in 0 chains, 3443 seeds are put forward NCS extension: 14 residues added (6 deleted due to clashes), 3457 seeds are put forward Round 1: 199 peptides, 37 chains. Longest chain 11 peptides. Score 0.345 Round 2: 230 peptides, 37 chains. Longest chain 20 peptides. Score 0.440 Round 3: 244 peptides, 39 chains. Longest chain 20 peptides. Score 0.455 Round 4: 235 peptides, 37 chains. Longest chain 13 peptides. Score 0.454 Round 5: 231 peptides, 37 chains. Longest chain 14 peptides. Score 0.443 Taking the results from Round 3 Chains 39, Residues 205, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 7678 restraints for refining 3407 atoms. 6868 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2097 (Rfree = 0.000) for 3407 atoms. Found 15 (16 requested) and removed 26 (8 requested) atoms. Cycle 22: After refmac, R = 0.2091 (Rfree = 0.000) for 3369 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 23: After refmac, R = 0.1990 (Rfree = 0.000) for 3351 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 24: After refmac, R = 0.1978 (Rfree = 0.000) for 3326 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 25: After refmac, R = 0.1841 (Rfree = 0.000) for 3318 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.82 3.92 Search for helices and strands: 0 residues in 0 chains, 3476 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3498 seeds are put forward Round 1: 188 peptides, 37 chains. Longest chain 12 peptides. Score 0.309 Round 2: 214 peptides, 36 chains. Longest chain 12 peptides. Score 0.405 Round 3: 206 peptides, 35 chains. Longest chain 12 peptides. Score 0.394 Round 4: 214 peptides, 35 chains. Longest chain 12 peptides. Score 0.418 Round 5: 223 peptides, 33 chains. Longest chain 12 peptides. Score 0.470 Taking the results from Round 5 Chains 33, Residues 190, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8109 restraints for refining 3503 atoms. 7352 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2286 (Rfree = 0.000) for 3503 atoms. Found 16 (16 requested) and removed 42 (8 requested) atoms. Cycle 27: After refmac, R = 0.1981 (Rfree = 0.000) for 3455 atoms. Found 16 (16 requested) and removed 47 (8 requested) atoms. Cycle 28: After refmac, R = 0.2028 (Rfree = 0.000) for 3412 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 29: After refmac, R = 0.2006 (Rfree = 0.000) for 3399 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 30: After refmac, R = 0.1514 (Rfree = 0.000) for 3385 atoms. Found 4 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 3499 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3518 seeds are put forward Round 1: 174 peptides, 37 chains. Longest chain 9 peptides. Score 0.262 Round 2: 230 peptides, 40 chains. Longest chain 15 peptides. Score 0.401 Round 3: 209 peptides, 36 chains. Longest chain 9 peptides. Score 0.390 Round 4: 224 peptides, 36 chains. Longest chain 13 peptides. Score 0.435 Round 5: 228 peptides, 37 chains. Longest chain 14 peptides. Score 0.434 Taking the results from Round 4 Chains 36, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8249 restraints for refining 3521 atoms. 7533 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2064 (Rfree = 0.000) for 3521 atoms. Found 16 (16 requested) and removed 31 (8 requested) atoms. Cycle 32: After refmac, R = 0.1885 (Rfree = 0.000) for 3482 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 33: After refmac, R = 0.1868 (Rfree = 0.000) for 3467 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 34: After refmac, R = 0.1987 (Rfree = 0.000) for 3455 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 35: After refmac, R = 0.1960 (Rfree = 0.000) for 3439 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 3582 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3595 seeds are put forward Round 1: 144 peptides, 32 chains. Longest chain 7 peptides. Score 0.228 Round 2: 191 peptides, 35 chains. Longest chain 10 peptides. Score 0.347 Round 3: 201 peptides, 33 chains. Longest chain 12 peptides. Score 0.405 Round 4: 195 peptides, 31 chains. Longest chain 14 peptides. Score 0.414 Round 5: 180 peptides, 29 chains. Longest chain 12 peptides. Score 0.395 Taking the results from Round 4 Chains 31, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8286 restraints for refining 3480 atoms. 7661 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2261 (Rfree = 0.000) for 3480 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 37: After refmac, R = 0.1923 (Rfree = 0.000) for 3447 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 38: After refmac, R = 0.1838 (Rfree = 0.000) for 3427 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 39: After refmac, R = 0.1729 (Rfree = 0.000) for 3416 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1995 (Rfree = 0.000) for 3417 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 3.79 Search for helices and strands: 0 residues in 0 chains, 3512 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3529 seeds are put forward Round 1: 161 peptides, 34 chains. Longest chain 8 peptides. Score 0.260 Round 2: 182 peptides, 32 chains. Longest chain 10 peptides. Score 0.360 Round 3: 189 peptides, 33 chains. Longest chain 9 peptides. Score 0.368 Round 4: 188 peptides, 32 chains. Longest chain 14 peptides. Score 0.379 Round 5: 194 peptides, 31 chains. Longest chain 12 peptides. Score 0.411 Taking the results from Round 5 Chains 31, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8358 restraints for refining 3493 atoms. 7737 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2421 (Rfree = 0.000) for 3493 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 42: After refmac, R = 0.1950 (Rfree = 0.000) for 3463 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 43: After refmac, R = 0.1822 (Rfree = 0.000) for 3447 atoms. Found 5 (16 requested) and removed 17 (8 requested) atoms. Cycle 44: After refmac, R = 0.1840 (Rfree = 0.000) for 3431 atoms. Found 10 (16 requested) and removed 11 (8 requested) atoms. Cycle 45: After refmac, R = 0.1950 (Rfree = 0.000) for 3427 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.82 3.92 Search for helices and strands: 0 residues in 0 chains, 3517 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3530 seeds are put forward Round 1: 137 peptides, 30 chains. Longest chain 11 peptides. Score 0.233 Round 2: 179 peptides, 34 chains. Longest chain 15 peptides. Score 0.322 Round 3: 168 peptides, 31 chains. Longest chain 12 peptides. Score 0.328 Round 4: 169 peptides, 32 chains. Longest chain 13 peptides. Score 0.317 Round 5: 182 peptides, 34 chains. Longest chain 15 peptides. Score 0.332 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 148, 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 1vpm-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4611 reflections ( 97.44 % complete ) and 8763 restraints for refining 3614 atoms. 8205 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2191 (Rfree = 0.000) for 3614 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2144 (Rfree = 0.000) for 3590 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1930 (Rfree = 0.000) for 3568 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2118 (Rfree = 0.000) for 3550 atoms. TimeTaking 58.98