Sun 23 Dec 22:22:59 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 1vmi-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmi-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmi-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-3.4-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/1vmi-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-3.4-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 22:23:08 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/1vmi-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-3.4-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 295 and 0 Target number of residues in the AU: 295 Target solvent content: 0.6461 Checking the provided sequence file Detected sequence length: 355 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 355 Adjusted target solvent content: 0.57 Input MTZ file: 1vmi-3.4-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: 182 Cell parameters: 94.674 94.674 174.359 90.000 90.000 120.000 Input sequence file: 1vmi-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2840 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: 87.180 3.400 Wilson plot Bfac: 75.29 6850 reflections ( 99.69 % complete ) and 0 restraints for refining 3132 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3349 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2478 (Rfree = 0.000) for 3132 atoms. Found 10 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.15 Search for helices and strands: 0 residues in 0 chains, 3177 seeds are put forward Round 1: 189 peptides, 30 chains. Longest chain 14 peptides. Score 0.439 Round 2: 216 peptides, 27 chains. Longest chain 22 peptides. Score 0.566 Round 3: 229 peptides, 24 chains. Longest chain 23 peptides. Score 0.637 Round 4: 234 peptides, 23 chains. Longest chain 20 peptides. Score 0.660 Round 5: 235 peptides, 27 chains. Longest chain 27 peptides. Score 0.617 Taking the results from Round 4 Chains 25, Residues 211, Estimated correctness of the model 47.0 % 10 chains (104 residues) have been docked in sequence ------------------------------------------------------ 6850 reflections ( 99.69 % complete ) and 4769 restraints for refining 2569 atoms. 3600 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2989 (Rfree = 0.000) for 2569 atoms. Found 19 (19 requested) and removed 46 (9 requested) atoms. Cycle 2: After refmac, R = 0.2860 (Rfree = 0.000) for 2515 atoms. Found 12 (19 requested) and removed 18 (9 requested) atoms. Cycle 3: After refmac, R = 0.2781 (Rfree = 0.000) for 2492 atoms. Found 6 (18 requested) and removed 13 (9 requested) atoms. Cycle 4: After refmac, R = 0.2761 (Rfree = 0.000) for 2475 atoms. Found 8 (18 requested) and removed 10 (9 requested) atoms. Cycle 5: After refmac, R = 0.2716 (Rfree = 0.000) for 2468 atoms. Found 5 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.14 Search for helices and strands: 0 residues in 0 chains, 2569 seeds are put forward Round 1: 219 peptides, 28 chains. Longest chain 19 peptides. Score 0.561 Round 2: 232 peptides, 21 chains. Longest chain 32 peptides. Score 0.678 Round 3: 234 peptides, 24 chains. Longest chain 22 peptides. Score 0.649 Round 4: 227 peptides, 21 chains. Longest chain 32 peptides. Score 0.666 Round 5: 230 peptides, 25 chains. Longest chain 26 peptides. Score 0.628 Taking the results from Round 2 Chains 26, Residues 211, Estimated correctness of the model 52.0 % 6 chains (62 residues) have been docked in sequence ------------------------------------------------------ 6850 reflections ( 99.69 % complete ) and 4804 restraints for refining 2465 atoms. 3806 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2771 (Rfree = 0.000) for 2465 atoms. Found 18 (18 requested) and removed 38 (9 requested) atoms. Cycle 7: After refmac, R = 0.2562 (Rfree = 0.000) for 2431 atoms. Found 9 (18 requested) and removed 15 (9 requested) atoms. Cycle 8: After refmac, R = 0.2419 (Rfree = 0.000) for 2406 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. Cycle 9: After refmac, R = 0.2333 (Rfree = 0.000) for 2390 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.2220 (Rfree = 0.000) for 2384 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.12 Search for helices and strands: 0 residues in 0 chains, 2469 seeds are put forward Round 1: 229 peptides, 22 chains. Longest chain 36 peptides. Score 0.660 Round 2: 245 peptides, 19 chains. Longest chain 22 peptides. Score 0.726 Round 3: 241 peptides, 22 chains. Longest chain 21 peptides. Score 0.687 Round 4: 231 peptides, 22 chains. Longest chain 26 peptides. Score 0.665 Round 5: 227 peptides, 18 chains. Longest chain 35 peptides. Score 0.699 Taking the results from Round 2 Chains 25, Residues 226, Estimated correctness of the model 64.3 % 5 chains (60 residues) have been docked in sequence Building loops using Loopy2018 25 chains (226 residues) following loop building 5 chains (60 residues) in sequence following loop building ------------------------------------------------------ 6850 reflections ( 99.69 % complete ) and 4627 restraints for refining 2443 atoms. 3559 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2673 (Rfree = 0.000) for 2443 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 12: After refmac, R = 0.2366 (Rfree = 0.000) for 2420 atoms. Found 6 (18 requested) and removed 16 (9 requested) atoms. Cycle 13: After refmac, R = 0.2291 (Rfree = 0.000) for 2388 atoms. Found 5 (17 requested) and removed 13 (9 requested) atoms. Cycle 14: After refmac, R = 0.2227 (Rfree = 0.000) for 2372 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 15: After refmac, R = 0.2159 (Rfree = 0.000) for 2361 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 2426 seeds are put forward Round 1: 217 peptides, 28 chains. Longest chain 22 peptides. Score 0.555 Round 2: 232 peptides, 23 chains. Longest chain 32 peptides. Score 0.656 Round 3: 238 peptides, 26 chains. Longest chain 24 peptides. Score 0.636 Round 4: 252 peptides, 22 chains. Longest chain 26 peptides. Score 0.711 Round 5: 243 peptides, 23 chains. Longest chain 30 peptides. Score 0.681 Taking the results from Round 4 Chains 28, Residues 230, Estimated correctness of the model 60.7 % 8 chains (103 residues) have been docked in sequence Building loops using Loopy2018 28 chains (230 residues) following loop building 8 chains (103 residues) in sequence following loop building ------------------------------------------------------ 6850 reflections ( 99.69 % complete ) and 4377 restraints for refining 2516 atoms. 3118 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2683 (Rfree = 0.000) for 2516 atoms. Found 16 (16 requested) and removed 31 (9 requested) atoms. Cycle 17: After refmac, R = 0.2508 (Rfree = 0.000) for 2482 atoms. Found 8 (16 requested) and removed 15 (9 requested) atoms. Cycle 18: After refmac, R = 0.2413 (Rfree = 0.000) for 2463 atoms. Found 7 (15 requested) and removed 17 (9 requested) atoms. Cycle 19: After refmac, R = 0.2351 (Rfree = 0.000) for 2450 atoms. Found 5 (15 requested) and removed 12 (9 requested) atoms. Cycle 20: After refmac, R = 0.2297 (Rfree = 0.000) for 2438 atoms. Found 3 (15 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.13 Search for helices and strands: 0 residues in 0 chains, 2513 seeds are put forward Round 1: 221 peptides, 27 chains. Longest chain 16 peptides. Score 0.580 Round 2: 247 peptides, 23 chains. Longest chain 31 peptides. Score 0.690 Round 3: 231 peptides, 24 chains. Longest chain 24 peptides. Score 0.642 Round 4: 247 peptides, 21 chains. Longest chain 25 peptides. Score 0.710 Round 5: 251 peptides, 21 chains. Longest chain 28 peptides. Score 0.719 Taking the results from Round 5 Chains 24, Residues 230, Estimated correctness of the model 62.6 % 5 chains (65 residues) have been docked in sequence Building loops using Loopy2018 24 chains (230 residues) following loop building 5 chains (65 residues) in sequence following loop building ------------------------------------------------------ 6850 reflections ( 99.69 % complete ) and 4891 restraints for refining 2583 atoms. 3750 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2883 (Rfree = 0.000) for 2583 atoms. Found 15 (15 requested) and removed 24 (9 requested) atoms. Cycle 22: After refmac, R = 0.2607 (Rfree = 0.000) for 2558 atoms. Found 7 (15 requested) and removed 19 (9 requested) atoms. Cycle 23: After refmac, R = 0.2473 (Rfree = 0.000) for 2532 atoms. Found 8 (14 requested) and removed 20 (9 requested) atoms. Cycle 24: After refmac, R = 0.2431 (Rfree = 0.000) for 2511 atoms. Found 7 (14 requested) and removed 12 (9 requested) atoms. Cycle 25: After refmac, R = 0.2463 (Rfree = 0.000) for 2499 atoms. Found 2 (13 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.18 Search for helices and strands: 0 residues in 0 chains, 2562 seeds are put forward Round 1: 209 peptides, 27 chains. Longest chain 35 peptides. Score 0.545 Round 2: 224 peptides, 26 chains. Longest chain 26 peptides. Score 0.600 Round 3: 225 peptides, 26 chains. Longest chain 27 peptides. Score 0.603 Round 4: 228 peptides, 25 chains. Longest chain 25 peptides. Score 0.623 Round 5: 216 peptides, 25 chains. Longest chain 17 peptides. Score 0.591 Taking the results from Round 4 Chains 26, Residues 203, Estimated correctness of the model 36.0 % 8 chains (86 residues) have been docked in sequence ------------------------------------------------------ 6850 reflections ( 99.69 % complete ) and 4782 restraints for refining 2583 atoms. 3698 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2699 (Rfree = 0.000) for 2583 atoms. Found 10 (13 requested) and removed 51 (9 requested) atoms. Cycle 27: After refmac, R = 0.2455 (Rfree = 0.000) for 2523 atoms. Found 5 (13 requested) and removed 17 (9 requested) atoms. Cycle 28: After refmac, R = 0.2396 (Rfree = 0.000) for 2494 atoms. Found 4 (13 requested) and removed 13 (9 requested) atoms. Cycle 29: After refmac, R = 0.2346 (Rfree = 0.000) for 2476 atoms. Found 8 (13 requested) and removed 16 (9 requested) atoms. Cycle 30: After refmac, R = 0.2327 (Rfree = 0.000) for 2460 atoms. Found 6 (13 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.15 Search for helices and strands: 0 residues in 0 chains, 2540 seeds are put forward Round 1: 216 peptides, 30 chains. Longest chain 22 peptides. Score 0.526 Round 2: 222 peptides, 29 chains. Longest chain 24 peptides. Score 0.557 Round 3: 222 peptides, 30 chains. Longest chain 18 peptides. Score 0.544 Round 4: 223 peptides, 28 chains. Longest chain 16 peptides. Score 0.573 Failed to save intermediate PDB Round 5: 231 peptides, 26 chains. Longest chain 19 peptides. Score 0.619 Taking the results from Round 5 Chains 32, Residues 205, Estimated correctness of the model 34.8 % 5 chains (48 residues) have been docked in sequence ------------------------------------------------------ 6850 reflections ( 99.69 % complete ) and 5278 restraints for refining 2582 atoms. 4335 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2703 (Rfree = 0.000) for 2582 atoms. Found 13 (13 requested) and removed 14 (9 requested) atoms. Cycle 32: After refmac, R = 0.2492 (Rfree = 0.000) for 2562 atoms. Found 6 (13 requested) and removed 11 (9 requested) atoms. Cycle 33: After refmac, R = 0.2387 (Rfree = 0.000) for 2546 atoms. Found 2 (13 requested) and removed 12 (9 requested) atoms. Cycle 34: After refmac, R = 0.2316 (Rfree = 0.000) for 2526 atoms. Found 6 (13 requested) and removed 14 (9 requested) atoms. Cycle 35: After refmac, R = 0.2272 (Rfree = 0.000) for 2513 atoms. Found 1 (13 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.14 Search for helices and strands: 0 residues in 0 chains, 2604 seeds are put forward Round 1: 179 peptides, 26 chains. Longest chain 18 peptides. Score 0.465 Round 2: 210 peptides, 26 chains. Longest chain 28 peptides. Score 0.561 Round 3: 210 peptides, 25 chains. Longest chain 26 peptides. Score 0.574 Round 4: 218 peptides, 29 chains. Longest chain 19 peptides. Score 0.545 Round 5: 210 peptides, 24 chains. Longest chain 19 peptides. Score 0.587 Taking the results from Round 5 Chains 28, Residues 186, Estimated correctness of the model 24.4 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6850 reflections ( 99.69 % complete ) and 5643 restraints for refining 2583 atoms. 4826 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2604 (Rfree = 0.000) for 2583 atoms. Found 13 (13 requested) and removed 11 (9 requested) atoms. Cycle 37: After refmac, R = 0.2439 (Rfree = 0.000) for 2572 atoms. Found 6 (13 requested) and removed 10 (9 requested) atoms. Cycle 38: After refmac, R = 0.2291 (Rfree = 0.000) for 2564 atoms. Found 4 (13 requested) and removed 11 (9 requested) atoms. Cycle 39: After refmac, R = 0.2263 (Rfree = 0.000) for 2549 atoms. Found 3 (13 requested) and removed 11 (9 requested) atoms. Cycle 40: After refmac, R = 0.2220 (Rfree = 0.000) for 2537 atoms. Found 3 (13 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.12 Search for helices and strands: 0 residues in 0 chains, 2618 seeds are put forward Round 1: 187 peptides, 31 chains. Longest chain 18 peptides. Score 0.417 Round 2: 210 peptides, 25 chains. Longest chain 17 peptides. Score 0.574 Round 3: 224 peptides, 28 chains. Longest chain 20 peptides. Score 0.575 Round 4: 211 peptides, 22 chains. Longest chain 20 peptides. Score 0.615 Round 5: 199 peptides, 21 chains. Longest chain 19 peptides. Score 0.595 Taking the results from Round 4 Chains 26, Residues 189, Estimated correctness of the model 33.5 % 5 chains (48 residues) have been docked in sequence ------------------------------------------------------ 6850 reflections ( 99.69 % complete ) and 5368 restraints for refining 2583 atoms. 4478 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2574 (Rfree = 0.000) for 2583 atoms. Found 13 (13 requested) and removed 13 (9 requested) atoms. Cycle 42: After refmac, R = 0.2365 (Rfree = 0.000) for 2573 atoms. Found 3 (13 requested) and removed 13 (9 requested) atoms. Cycle 43: After refmac, R = 0.2281 (Rfree = 0.000) for 2556 atoms. Found 5 (13 requested) and removed 17 (9 requested) atoms. Cycle 44: After refmac, R = 0.2272 (Rfree = 0.000) for 2543 atoms. Found 3 (13 requested) and removed 10 (9 requested) atoms. Cycle 45: After refmac, R = 0.2273 (Rfree = 0.000) for 2533 atoms. Found 3 (13 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.14 Search for helices and strands: 0 residues in 0 chains, 2613 seeds are put forward Round 1: 186 peptides, 29 chains. Longest chain 20 peptides. Score 0.444 Round 2: 210 peptides, 26 chains. Longest chain 20 peptides. Score 0.561 Round 3: 212 peptides, 26 chains. Longest chain 16 peptides. Score 0.567 Round 4: 222 peptides, 22 chains. Longest chain 30 peptides. Score 0.643 Round 5: 217 peptides, 26 chains. Longest chain 21 peptides. Score 0.581 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 200, Estimated correctness of the model 42.1 % 2 chains (33 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 1vmi-3_warpNtrace.pdb as input Building loops using Loopy2018 23 chains (200 residues) following loop building 2 chains (33 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6850 reflections ( 99.69 % complete ) and 5380 restraints for refining 2583 atoms. 4468 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2720 (Rfree = 0.000) for 2583 atoms. Found 0 (13 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2596 (Rfree = 0.000) for 2563 atoms. Found 0 (13 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2552 (Rfree = 0.000) for 2549 atoms. Found 0 (13 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2539 (Rfree = 0.000) for 2536 atoms. TimeTaking 59.2