Sun 23 Dec 22:22:55 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 2fea-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fea-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fea-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-3.2-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/2fea-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-3.2-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 22:23:04 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/2fea-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-3.2-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 390 and 0 Target number of residues in the AU: 390 Target solvent content: 0.6168 Checking the provided sequence file Detected sequence length: 236 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 472 Adjusted target solvent content: 0.54 Input MTZ file: 2fea-3.2-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: 4 Cell parameters: 59.005 43.112 109.575 90.000 98.912 90.000 Input sequence file: 2fea-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3776 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 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: 22.949 3.200 Wilson plot Bfac: 59.58 9144 reflections ( 98.33 % complete ) and 0 restraints for refining 4204 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3130 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2508 (Rfree = 0.000) for 4204 atoms. Found 37 (37 requested) and removed 50 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 2.89 Search for helices and strands: 0 residues in 0 chains, 4301 seeds are put forward NCS extension: 0 residues added, 4301 seeds are put forward Round 1: 260 peptides, 46 chains. Longest chain 20 peptides. Score 0.408 Round 2: 294 peptides, 37 chains. Longest chain 37 peptides. Score 0.593 Round 3: 309 peptides, 36 chains. Longest chain 18 peptides. Score 0.634 Round 4: 317 peptides, 32 chains. Longest chain 36 peptides. Score 0.685 Round 5: 332 peptides, 35 chains. Longest chain 25 peptides. Score 0.686 Taking the results from Round 5 Chains 35, Residues 297, Estimated correctness of the model 62.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9144 reflections ( 98.33 % complete ) and 7462 restraints for refining 3446 atoms. 6309 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2565 (Rfree = 0.000) for 3446 atoms. Found 30 (30 requested) and removed 23 (15 requested) atoms. Cycle 2: After refmac, R = 0.2387 (Rfree = 0.000) for 3421 atoms. Found 19 (30 requested) and removed 18 (15 requested) atoms. Cycle 3: After refmac, R = 0.2265 (Rfree = 0.000) for 3407 atoms. Found 7 (30 requested) and removed 16 (15 requested) atoms. Cycle 4: After refmac, R = 0.2201 (Rfree = 0.000) for 3391 atoms. Found 8 (30 requested) and removed 15 (15 requested) atoms. Cycle 5: After refmac, R = 0.2266 (Rfree = 0.000) for 3380 atoms. Found 4 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 3511 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 3532 seeds are put forward Round 1: 311 peptides, 40 chains. Longest chain 32 peptides. Score 0.601 Round 2: 329 peptides, 35 chains. Longest chain 31 peptides. Score 0.681 Round 3: 332 peptides, 34 chains. Longest chain 27 peptides. Score 0.695 Round 4: 347 peptides, 34 chains. Longest chain 31 peptides. Score 0.720 Round 5: 337 peptides, 33 chains. Longest chain 39 peptides. Score 0.711 Taking the results from Round 4 Chains 35, Residues 313, Estimated correctness of the model 69.3 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7071 restraints for refining 3446 atoms. 5752 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2461 (Rfree = 0.000) for 3446 atoms. Found 23 (30 requested) and removed 21 (15 requested) atoms. Cycle 7: After refmac, R = 0.2396 (Rfree = 0.000) for 3437 atoms. Found 18 (29 requested) and removed 23 (15 requested) atoms. Cycle 8: After refmac, R = 0.2186 (Rfree = 0.000) for 3420 atoms. Found 5 (29 requested) and removed 17 (15 requested) atoms. Cycle 9: After refmac, R = 0.2131 (Rfree = 0.000) for 3404 atoms. Found 8 (28 requested) and removed 15 (15 requested) atoms. Cycle 10: After refmac, R = 0.2096 (Rfree = 0.000) for 3394 atoms. Found 4 (28 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 2.91 Search for helices and strands: 0 residues in 0 chains, 3505 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 3522 seeds are put forward Round 1: 300 peptides, 35 chains. Longest chain 27 peptides. Score 0.625 Round 2: 316 peptides, 31 chains. Longest chain 31 peptides. Score 0.691 Round 3: 327 peptides, 31 chains. Longest chain 32 peptides. Score 0.710 Round 4: 334 peptides, 33 chains. Longest chain 33 peptides. Score 0.706 Round 5: 342 peptides, 31 chains. Longest chain 31 peptides. Score 0.734 Taking the results from Round 5 Chains 35, Residues 311, Estimated correctness of the model 72.1 % 4 chains (70 residues) have been docked in sequence Building loops using Loopy2018 35 chains (311 residues) following loop building 4 chains (70 residues) in sequence following loop building ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 6609 restraints for refining 3447 atoms. 5133 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2535 (Rfree = 0.000) for 3447 atoms. Found 27 (27 requested) and removed 32 (15 requested) atoms. Cycle 12: After refmac, R = 0.2404 (Rfree = 0.000) for 3435 atoms. Found 18 (26 requested) and removed 23 (15 requested) atoms. Cycle 13: After refmac, R = 0.2252 (Rfree = 0.000) for 3416 atoms. Found 7 (26 requested) and removed 17 (15 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2197 (Rfree = 0.000) for 3400 atoms. Found 7 (25 requested) and removed 16 (15 requested) atoms. Cycle 15: After refmac, R = 0.2224 (Rfree = 0.000) for 3385 atoms. Found 9 (25 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.11 2.95 Search for helices and strands: 0 residues in 0 chains, 3502 seeds are put forward NCS extension: 32 residues added (5 deleted due to clashes), 3534 seeds are put forward Round 1: 313 peptides, 37 chains. Longest chain 24 peptides. Score 0.633 Round 2: 331 peptides, 32 chains. Longest chain 30 peptides. Score 0.709 Round 3: 319 peptides, 33 chains. Longest chain 30 peptides. Score 0.680 Round 4: 318 peptides, 33 chains. Longest chain 22 peptides. Score 0.678 Round 5: 331 peptides, 31 chains. Longest chain 26 peptides. Score 0.717 Taking the results from Round 5 Chains 34, Residues 300, Estimated correctness of the model 68.7 % 2 chains (25 residues) have been docked in sequence Building loops using Loopy2018 34 chains (300 residues) following loop building 2 chains (25 residues) in sequence following loop building ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7169 restraints for refining 3447 atoms. 5892 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2675 (Rfree = 0.000) for 3447 atoms. Found 24 (24 requested) and removed 21 (15 requested) atoms. Cycle 17: After refmac, R = 0.2492 (Rfree = 0.000) for 3445 atoms. Found 19 (23 requested) and removed 16 (15 requested) atoms. Cycle 18: After refmac, R = 0.2234 (Rfree = 0.000) for 3443 atoms. Found 6 (23 requested) and removed 16 (15 requested) atoms. Cycle 19: After refmac, R = 0.2166 (Rfree = 0.000) for 3430 atoms. Found 7 (22 requested) and removed 15 (15 requested) atoms. Cycle 20: After refmac, R = 0.2178 (Rfree = 0.000) for 3421 atoms. Found 7 (22 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.10 2.94 Search for helices and strands: 0 residues in 0 chains, 3541 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3557 seeds are put forward Round 1: 279 peptides, 33 chains. Longest chain 26 peptides. Score 0.600 Round 2: 298 peptides, 29 chains. Longest chain 25 peptides. Score 0.676 Round 3: 307 peptides, 28 chains. Longest chain 28 peptides. Score 0.701 Round 4: 305 peptides, 34 chains. Longest chain 28 peptides. Score 0.645 Round 5: 293 peptides, 33 chains. Longest chain 22 peptides. Score 0.630 Taking the results from Round 3 Chains 28, Residues 279, Estimated correctness of the model 65.4 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7456 restraints for refining 3447 atoms. 6301 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2303 (Rfree = 0.000) for 3447 atoms. Found 21 (21 requested) and removed 16 (15 requested) atoms. Cycle 22: After refmac, R = 0.2158 (Rfree = 0.000) for 3447 atoms. Found 17 (20 requested) and removed 16 (15 requested) atoms. Cycle 23: After refmac, R = 0.2078 (Rfree = 0.000) for 3447 atoms. Found 5 (20 requested) and removed 15 (15 requested) atoms. Cycle 24: After refmac, R = 0.2060 (Rfree = 0.000) for 3433 atoms. Found 4 (19 requested) and removed 15 (15 requested) atoms. Cycle 25: After refmac, R = 0.2064 (Rfree = 0.000) for 3422 atoms. Found 2 (19 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 2.96 Search for helices and strands: 0 residues in 0 chains, 3496 seeds are put forward NCS extension: 36 residues added (5 deleted due to clashes), 3532 seeds are put forward Round 1: 296 peptides, 34 chains. Longest chain 28 peptides. Score 0.626 Round 2: 309 peptides, 35 chains. Longest chain 36 peptides. Score 0.643 Round 3: 325 peptides, 34 chains. Longest chain 36 peptides. Score 0.682 Round 4: 330 peptides, 27 chains. Longest chain 36 peptides. Score 0.745 Round 5: 308 peptides, 38 chains. Longest chain 28 peptides. Score 0.614 Taking the results from Round 4 Chains 28, Residues 303, Estimated correctness of the model 74.1 % 3 chains (64 residues) have been docked in sequence Building loops using Loopy2018 28 chains (303 residues) following loop building 3 chains (64 residues) in sequence following loop building ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 6642 restraints for refining 3446 atoms. 5195 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2366 (Rfree = 0.000) for 3446 atoms. Found 18 (18 requested) and removed 27 (15 requested) atoms. Cycle 27: After refmac, R = 0.2192 (Rfree = 0.000) for 3423 atoms. Found 8 (17 requested) and removed 17 (15 requested) atoms. Cycle 28: After refmac, R = 0.2139 (Rfree = 0.000) for 3410 atoms. Found 7 (17 requested) and removed 15 (15 requested) atoms. Cycle 29: After refmac, R = 0.2115 (Rfree = 0.000) for 3402 atoms. Found 2 (16 requested) and removed 15 (15 requested) atoms. Cycle 30: After refmac, R = 0.2097 (Rfree = 0.000) for 3389 atoms. Found 4 (16 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.12 2.96 Search for helices and strands: 0 residues in 0 chains, 3475 seeds are put forward NCS extension: 31 residues added (22 deleted due to clashes), 3506 seeds are put forward Round 1: 288 peptides, 39 chains. Longest chain 25 peptides. Score 0.559 Round 2: 305 peptides, 35 chains. Longest chain 27 peptides. Score 0.635 Round 3: 285 peptides, 32 chains. Longest chain 27 peptides. Score 0.623 Round 4: 304 peptides, 41 chains. Longest chain 23 peptides. Score 0.576 Round 5: 306 peptides, 36 chains. Longest chain 20 peptides. Score 0.628 Taking the results from Round 2 Chains 37, Residues 270, Estimated correctness of the model 50.2 % 3 chains (43 residues) have been docked in sequence Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7044 restraints for refining 3446 atoms. 5801 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2387 (Rfree = 0.000) for 3446 atoms. Found 15 (15 requested) and removed 21 (15 requested) atoms. Cycle 32: After refmac, R = 0.2223 (Rfree = 0.000) for 3433 atoms. Found 11 (15 requested) and removed 15 (15 requested) atoms. Cycle 33: After refmac, R = 0.2184 (Rfree = 0.000) for 3429 atoms. Found 9 (15 requested) and removed 16 (15 requested) atoms. Cycle 34: After refmac, R = 0.2171 (Rfree = 0.000) for 3420 atoms. Found 9 (15 requested) and removed 16 (15 requested) atoms. Cycle 35: After refmac, R = 0.2143 (Rfree = 0.000) for 3412 atoms. Found 8 (15 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 2.95 Search for helices and strands: 0 residues in 0 chains, 3510 seeds are put forward NCS extension: 14 residues added (7 deleted due to clashes), 3524 seeds are put forward Round 1: 255 peptides, 38 chains. Longest chain 20 peptides. Score 0.489 Round 2: 278 peptides, 34 chains. Longest chain 24 peptides. Score 0.588 Round 3: 285 peptides, 33 chains. Longest chain 27 peptides. Score 0.613 Round 4: 276 peptides, 34 chains. Longest chain 33 peptides. Score 0.583 Round 5: 290 peptides, 31 chains. Longest chain 27 peptides. Score 0.642 Taking the results from Round 5 Chains 32, Residues 259, Estimated correctness of the model 51.9 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7427 restraints for refining 3447 atoms. 6332 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2341 (Rfree = 0.000) for 3447 atoms. Found 15 (15 requested) and removed 20 (15 requested) atoms. Cycle 37: After refmac, R = 0.2242 (Rfree = 0.000) for 3438 atoms. Found 15 (15 requested) and removed 15 (15 requested) atoms. Cycle 38: After refmac, R = 0.2172 (Rfree = 0.000) for 3437 atoms. Found 4 (15 requested) and removed 16 (15 requested) atoms. Cycle 39: After refmac, R = 0.2133 (Rfree = 0.000) for 3425 atoms. Found 5 (15 requested) and removed 15 (15 requested) atoms. Cycle 40: After refmac, R = 0.2080 (Rfree = 0.000) for 3415 atoms. Found 4 (15 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 2.95 Search for helices and strands: 0 residues in 0 chains, 3505 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3524 seeds are put forward Round 1: 248 peptides, 37 chains. Longest chain 20 peptides. Score 0.482 Round 2: 272 peptides, 36 chains. Longest chain 25 peptides. Score 0.553 Round 3: 292 peptides, 39 chains. Longest chain 32 peptides. Score 0.569 Round 4: 278 peptides, 36 chains. Longest chain 20 peptides. Score 0.567 Round 5: 281 peptides, 40 chains. Longest chain 23 peptides. Score 0.532 Taking the results from Round 3 Chains 41, Residues 253, Estimated correctness of the model 32.4 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7492 restraints for refining 3447 atoms. 6446 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2244 (Rfree = 0.000) for 3447 atoms. Found 15 (15 requested) and removed 17 (15 requested) atoms. Cycle 42: After refmac, R = 0.2099 (Rfree = 0.000) for 3445 atoms. Found 14 (15 requested) and removed 15 (15 requested) atoms. Cycle 43: After refmac, R = 0.2025 (Rfree = 0.000) for 3443 atoms. Found 5 (15 requested) and removed 15 (15 requested) atoms. Cycle 44: After refmac, R = 0.1979 (Rfree = 0.000) for 3430 atoms. Found 3 (15 requested) and removed 15 (15 requested) atoms. Cycle 45: After refmac, R = 0.1930 (Rfree = 0.000) for 3416 atoms. Found 7 (15 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 2.94 Search for helices and strands: 0 residues in 0 chains, 3528 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3551 seeds are put forward Round 1: 236 peptides, 36 chains. Longest chain 24 peptides. Score 0.461 Round 2: 262 peptides, 36 chains. Longest chain 29 peptides. Score 0.529 Round 3: 270 peptides, 36 chains. Longest chain 25 peptides. Score 0.548 Round 4: 277 peptides, 33 chains. Longest chain 27 peptides. Score 0.596 Round 5: 281 peptides, 33 chains. Longest chain 28 peptides. Score 0.604 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 248, Estimated correctness of the model 42.1 % 3 chains (57 residues) have been docked in sequence Sequence coverage is 22 % Consider running further cycles of model building using 2fea-3_warpNtrace.pdb as input Building loops using Loopy2018 34 chains (248 residues) following loop building 3 chains (57 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9144 reflections ( 98.33 % complete ) and 6961 restraints for refining 3447 atoms. 5739 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2385 (Rfree = 0.000) for 3447 atoms. Found 0 (15 requested) and removed 10 (15 requested) atoms. Cycle 47: After refmac, R = 0.2281 (Rfree = 0.000) for 3428 atoms. Found 0 (15 requested) and removed 2 (15 requested) atoms. Cycle 48: After refmac, R = 0.2235 (Rfree = 0.000) for 3424 atoms. Found 0 (15 requested) and removed 1 (15 requested) atoms. Cycle 49: After refmac, R = 0.2215 (Rfree = 0.000) for 3421 atoms. TimeTaking 57.6