Sun 23 Dec 22:23:05 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 1zbt-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zbt-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zbt-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-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/1zbt-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-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 22:23:15 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/1zbt-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-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 303 and 0 Target number of residues in the AU: 303 Target solvent content: 0.6603 Checking the provided sequence file Detected sequence length: 371 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 371 Adjusted target solvent content: 0.58 Input MTZ file: 1zbt-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: 96 Cell parameters: 71.823 71.823 187.134 90.000 90.000 90.000 Input sequence file: 1zbt-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2968 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: 28.608 4.000 Wilson plot Bfac: 85.09 4532 reflections ( 99.56 % complete ) and 0 restraints for refining 3281 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3441 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3553 (Rfree = 0.000) for 3281 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.88 3.48 Search for helices and strands: 0 residues in 0 chains, 3335 seeds are put forward Round 1: 145 peptides, 20 chains. Longest chain 13 peptides. Score 0.429 Round 2: 161 peptides, 19 chains. Longest chain 19 peptides. Score 0.496 Round 3: 163 peptides, 18 chains. Longest chain 25 peptides. Score 0.516 Round 4: 168 peptides, 20 chains. Longest chain 23 peptides. Score 0.503 Round 5: 172 peptides, 17 chains. Longest chain 18 peptides. Score 0.556 Taking the results from Round 5 Chains 22, Residues 155, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 4532 reflections ( 99.56 % complete ) and 5427 restraints for refining 2499 atoms. 4661 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2866 (Rfree = 0.000) for 2499 atoms. Found 11 (11 requested) and removed 29 (5 requested) atoms. Cycle 2: After refmac, R = 0.2655 (Rfree = 0.000) for 2427 atoms. Found 9 (11 requested) and removed 23 (5 requested) atoms. Cycle 3: After refmac, R = 0.2647 (Rfree = 0.000) for 2385 atoms. Found 6 (11 requested) and removed 13 (5 requested) atoms. Cycle 4: After refmac, R = 0.2542 (Rfree = 0.000) for 2351 atoms. Found 4 (11 requested) and removed 19 (5 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2455 (Rfree = 0.000) for 2314 atoms. Found 4 (11 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 3.39 Search for helices and strands: 0 residues in 0 chains, 2419 seeds are put forward Round 1: 170 peptides, 24 chains. Longest chain 13 peptides. Score 0.451 Round 2: 187 peptides, 20 chains. Longest chain 28 peptides. Score 0.558 Round 3: 194 peptides, 21 chains. Longest chain 18 peptides. Score 0.564 Round 4: 203 peptides, 20 chains. Longest chain 20 peptides. Score 0.600 Round 5: 194 peptides, 17 chains. Longest chain 42 peptides. Score 0.614 Taking the results from Round 5 Chains 21, Residues 177, Estimated correctness of the model 0.0 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 4532 reflections ( 99.56 % complete ) and 5385 restraints for refining 2589 atoms. 4530 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2749 (Rfree = 0.000) for 2589 atoms. Found 12 (12 requested) and removed 38 (6 requested) atoms. Cycle 7: After refmac, R = 0.2559 (Rfree = 0.000) for 2523 atoms. Found 9 (12 requested) and removed 18 (6 requested) atoms. Cycle 8: After refmac, R = 0.2528 (Rfree = 0.000) for 2492 atoms. Found 3 (11 requested) and removed 19 (5 requested) atoms. Cycle 9: After refmac, R = 0.2610 (Rfree = 0.000) for 2461 atoms. Found 6 (11 requested) and removed 22 (5 requested) atoms. Cycle 10: After refmac, R = 0.2420 (Rfree = 0.000) for 2437 atoms. Found 4 (11 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.36 Search for helices and strands: 0 residues in 0 chains, 2525 seeds are put forward Round 1: 154 peptides, 22 chains. Longest chain 17 peptides. Score 0.429 Round 2: 177 peptides, 18 chains. Longest chain 33 peptides. Score 0.556 Round 3: 187 peptides, 21 chains. Longest chain 34 peptides. Score 0.545 Round 4: 169 peptides, 17 chains. Longest chain 20 peptides. Score 0.547 Round 5: 170 peptides, 21 chains. Longest chain 24 peptides. Score 0.495 Taking the results from Round 2 Chains 20, Residues 159, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4532 reflections ( 99.56 % complete ) and 5550 restraints for refining 2549 atoms. 4862 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2567 (Rfree = 0.000) for 2549 atoms. Found 8 (12 requested) and removed 28 (6 requested) atoms. Cycle 12: After refmac, R = 0.2499 (Rfree = 0.000) for 2506 atoms. Found 9 (12 requested) and removed 14 (6 requested) atoms. Cycle 13: After refmac, R = 0.2266 (Rfree = 0.000) for 2490 atoms. Found 2 (11 requested) and removed 12 (5 requested) atoms. Cycle 14: After refmac, R = 0.2287 (Rfree = 0.000) for 2458 atoms. Found 9 (11 requested) and removed 17 (5 requested) atoms. Cycle 15: After refmac, R = 0.2146 (Rfree = 0.000) for 2447 atoms. Found 6 (11 requested) and removed 17 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.79 3.40 Search for helices and strands: 0 residues in 0 chains, 2535 seeds are put forward Round 1: 158 peptides, 22 chains. Longest chain 14 peptides. Score 0.442 Round 2: 178 peptides, 21 chains. Longest chain 17 peptides. Score 0.519 Round 3: 177 peptides, 22 chains. Longest chain 20 peptides. Score 0.502 Round 4: 176 peptides, 19 chains. Longest chain 31 peptides. Score 0.540 Round 5: 181 peptides, 20 chains. Longest chain 37 peptides. Score 0.541 Taking the results from Round 5 Chains 21, Residues 161, Estimated correctness of the model 0.0 % 1 chains (31 residues) have been docked in sequence ------------------------------------------------------ 4532 reflections ( 99.56 % complete ) and 5819 restraints for refining 2679 atoms. 5055 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2580 (Rfree = 0.000) for 2679 atoms. Found 12 (12 requested) and removed 55 (6 requested) atoms. Cycle 17: After refmac, R = 0.2611 (Rfree = 0.000) for 2612 atoms. Found 12 (12 requested) and removed 29 (6 requested) atoms. Cycle 18: After refmac, R = 0.2372 (Rfree = 0.000) for 2579 atoms. Found 9 (12 requested) and removed 26 (6 requested) atoms. Cycle 19: After refmac, R = 0.2432 (Rfree = 0.000) for 2553 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 20: After refmac, R = 0.2199 (Rfree = 0.000) for 2534 atoms. Found 6 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.77 3.39 Search for helices and strands: 0 residues in 0 chains, 2637 seeds are put forward Round 1: 159 peptides, 26 chains. Longest chain 16 peptides. Score 0.384 Round 2: 174 peptides, 22 chains. Longest chain 28 peptides. Score 0.493 Round 3: 179 peptides, 25 chains. Longest chain 17 peptides. Score 0.466 Round 4: 173 peptides, 21 chains. Longest chain 18 peptides. Score 0.504 Round 5: 171 peptides, 22 chains. Longest chain 21 peptides. Score 0.483 Taking the results from Round 4 Chains 22, Residues 152, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4532 reflections ( 99.56 % complete ) and 5913 restraints for refining 2678 atoms. 5273 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2385 (Rfree = 0.000) for 2678 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. Cycle 22: After refmac, R = 0.2152 (Rfree = 0.000) for 2640 atoms. Found 2 (12 requested) and removed 15 (6 requested) atoms. Cycle 23: After refmac, R = 0.2092 (Rfree = 0.000) for 2619 atoms. Found 3 (12 requested) and removed 11 (6 requested) atoms. Cycle 24: After refmac, R = 0.2023 (Rfree = 0.000) for 2605 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.2073 (Rfree = 0.000) for 2587 atoms. Found 1 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.73 3.35 Search for helices and strands: 0 residues in 0 chains, 2694 seeds are put forward Round 1: 131 peptides, 20 chains. Longest chain 21 peptides. Score 0.380 Round 2: 161 peptides, 23 chains. Longest chain 15 peptides. Score 0.437 Round 3: 172 peptides, 23 chains. Longest chain 14 peptides. Score 0.472 Round 4: 176 peptides, 23 chains. Longest chain 22 peptides. Score 0.485 Round 5: 172 peptides, 23 chains. Longest chain 19 peptides. Score 0.472 Taking the results from Round 4 Chains 24, Residues 153, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4532 reflections ( 99.56 % complete ) and 6227 restraints for refining 2681 atoms. 5624 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2403 (Rfree = 0.000) for 2681 atoms. Found 6 (12 requested) and removed 23 (6 requested) atoms. Cycle 27: After refmac, R = 0.2733 (Rfree = 0.000) for 2643 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 28: After refmac, R = 0.2135 (Rfree = 0.000) for 2609 atoms. Found 4 (12 requested) and removed 11 (6 requested) atoms. Cycle 29: After refmac, R = 0.2143 (Rfree = 0.000) for 2587 atoms. Found 4 (12 requested) and removed 12 (6 requested) atoms. Cycle 30: After refmac, R = 0.2056 (Rfree = 0.000) for 2572 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 3.38 Search for helices and strands: 0 residues in 0 chains, 2680 seeds are put forward Round 1: 145 peptides, 28 chains. Longest chain 8 peptides. Score 0.302 Round 2: 174 peptides, 29 chains. Longest chain 13 peptides. Score 0.391 Round 3: 166 peptides, 26 chains. Longest chain 16 peptides. Score 0.408 Round 4: 169 peptides, 26 chains. Longest chain 21 peptides. Score 0.419 Round 5: 196 peptides, 24 chains. Longest chain 20 peptides. Score 0.530 Taking the results from Round 5 Chains 25, Residues 172, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4532 reflections ( 99.56 % complete ) and 5954 restraints for refining 2681 atoms. 5247 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2744 (Rfree = 0.000) for 2681 atoms. Found 11 (12 requested) and removed 19 (6 requested) atoms. Cycle 32: After refmac, R = 0.2450 (Rfree = 0.000) for 2653 atoms. Found 9 (12 requested) and removed 26 (6 requested) atoms. Cycle 33: After refmac, R = 0.2330 (Rfree = 0.000) for 2619 atoms. Found 4 (12 requested) and removed 11 (6 requested) atoms. Cycle 34: After refmac, R = 0.2297 (Rfree = 0.000) for 2609 atoms. Found 3 (12 requested) and removed 16 (6 requested) atoms. Cycle 35: After refmac, R = 0.2262 (Rfree = 0.000) for 2592 atoms. Found 3 (12 requested) and removed 22 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.43 Search for helices and strands: 0 residues in 0 chains, 2684 seeds are put forward Round 1: 148 peptides, 28 chains. Longest chain 16 peptides. Score 0.313 Round 2: 152 peptides, 22 chains. Longest chain 16 peptides. Score 0.422 Round 3: 154 peptides, 23 chains. Longest chain 17 peptides. Score 0.413 Round 4: 152 peptides, 24 chains. Longest chain 17 peptides. Score 0.391 Round 5: 156 peptides, 21 chains. Longest chain 26 peptides. Score 0.450 Taking the results from Round 5 Chains 21, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4532 reflections ( 99.56 % complete ) and 6332 restraints for refining 2681 atoms. 5813 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2526 (Rfree = 0.000) for 2681 atoms. Found 11 (12 requested) and removed 21 (6 requested) atoms. Cycle 37: After refmac, R = 0.2320 (Rfree = 0.000) for 2663 atoms. Found 2 (12 requested) and removed 14 (6 requested) atoms. Cycle 38: After refmac, R = 0.2295 (Rfree = 0.000) for 2642 atoms. Found 5 (12 requested) and removed 16 (6 requested) atoms. Cycle 39: After refmac, R = 0.2247 (Rfree = 0.000) for 2629 atoms. Found 3 (12 requested) and removed 24 (6 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2142 (Rfree = 0.000) for 2605 atoms. Found 1 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.83 3.44 Search for helices and strands: 0 residues in 0 chains, 2707 seeds are put forward Round 1: 143 peptides, 27 chains. Longest chain 10 peptides. Score 0.311 Round 2: 157 peptides, 24 chains. Longest chain 13 peptides. Score 0.408 Round 3: 154 peptides, 25 chains. Longest chain 11 peptides. Score 0.382 Round 4: 162 peptides, 23 chains. Longest chain 12 peptides. Score 0.440 Round 5: 174 peptides, 25 chains. Longest chain 15 peptides. Score 0.450 Taking the results from Round 5 Chains 25, Residues 149, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4532 reflections ( 99.56 % complete ) and 6239 restraints for refining 2681 atoms. 5640 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2438 (Rfree = 0.000) for 2681 atoms. Found 9 (12 requested) and removed 17 (6 requested) atoms. Cycle 42: After refmac, R = 0.2241 (Rfree = 0.000) for 2640 atoms. Found 4 (12 requested) and removed 12 (6 requested) atoms. Cycle 43: After refmac, R = 0.2157 (Rfree = 0.000) for 2620 atoms. Found 0 (12 requested) and removed 8 (6 requested) atoms. Cycle 44: After refmac, R = 0.2122 (Rfree = 0.000) for 2607 atoms. Found 2 (12 requested) and removed 10 (6 requested) atoms. Cycle 45: After refmac, R = 0.2091 (Rfree = 0.000) for 2596 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 3.41 Search for helices and strands: 0 residues in 0 chains, 2700 seeds are put forward Round 1: 130 peptides, 25 chains. Longest chain 11 peptides. Score 0.294 Round 2: 140 peptides, 25 chains. Longest chain 12 peptides. Score 0.332 Round 3: 147 peptides, 23 chains. Longest chain 17 peptides. Score 0.389 Round 4: 142 peptides, 22 chains. Longest chain 17 peptides. Score 0.387 Round 5: 138 peptides, 23 chains. Longest chain 12 peptides. Score 0.357 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 124, 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 1zbt-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4532 reflections ( 99.56 % complete ) and 6345 restraints for refining 2681 atoms. 5872 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2455 (Rfree = 0.000) for 2681 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2541 (Rfree = 0.000) for 2653 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2363 (Rfree = 0.000) for 2638 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2246 (Rfree = 0.000) for 2623 atoms. TimeTaking 49.78