Tue 25 Dec 19:27:57 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 2p4g-2.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p4g-2.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p4g-2.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-2.5-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/2p4g-2.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-2.5-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 ============================================================ Tue 25 Dec 19:28:07 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/2p4g-2.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-2.5-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 337 and 0 Target number of residues in the AU: 337 Target solvent content: 0.5851 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 270 Adjusted target solvent content: 0.67 Input MTZ file: 2p4g-2.5-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: 172 Cell parameters: 115.650 115.650 56.930 90.000 90.000 120.000 Input sequence file: 2p4g-2.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 2160 target number of atoms Had to go as low as 1.05 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: 28.913 2.500 Wilson plot Bfac: 46.79 15130 reflections ( 99.41 % complete ) and 0 restraints for refining 2396 atoms. Observations/parameters ratio is 1.58 ------------------------------------------------------ Starting model: R = 0.3699 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3571 (Rfree = 0.000) for 2396 atoms. Found 43 (43 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.81 2.22 Round 1: 131 peptides, 22 chains. Longest chain 10 peptides. Score 0.359 Round 2: 158 peptides, 22 chains. Longest chain 19 peptides. Score 0.460 Round 3: 158 peptides, 16 chains. Longest chain 27 peptides. Score 0.552 Round 4: 165 peptides, 20 chains. Longest chain 20 peptides. Score 0.515 Round 5: 158 peptides, 19 chains. Longest chain 22 peptides. Score 0.507 Taking the results from Round 3 Chains 17, Residues 142, Estimated correctness of the model 66.8 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 15130 reflections ( 99.41 % complete ) and 4218 restraints for refining 2024 atoms. 3633 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3583 (Rfree = 0.000) for 2024 atoms. Found 33 (36 requested) and removed 19 (18 requested) atoms. Cycle 2: After refmac, R = 0.3352 (Rfree = 0.000) for 2036 atoms. Found 26 (36 requested) and removed 25 (18 requested) atoms. Cycle 3: After refmac, R = 0.3133 (Rfree = 0.000) for 2027 atoms. Found 14 (36 requested) and removed 18 (18 requested) atoms. Cycle 4: After refmac, R = 0.3081 (Rfree = 0.000) for 2019 atoms. Found 9 (36 requested) and removed 19 (18 requested) atoms. Cycle 5: After refmac, R = 0.2935 (Rfree = 0.000) for 2003 atoms. Found 11 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.68 2.12 Round 1: 159 peptides, 21 chains. Longest chain 27 peptides. Score 0.479 Round 2: 167 peptides, 22 chains. Longest chain 16 peptides. Score 0.491 Round 3: 162 peptides, 19 chains. Longest chain 20 peptides. Score 0.520 Round 4: 161 peptides, 18 chains. Longest chain 18 peptides. Score 0.532 Round 5: 160 peptides, 16 chains. Longest chain 22 peptides. Score 0.558 Taking the results from Round 5 Chains 18, Residues 144, Estimated correctness of the model 67.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 15130 reflections ( 99.41 % complete ) and 4226 restraints for refining 2022 atoms. 3641 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3194 (Rfree = 0.000) for 2022 atoms. Found 27 (36 requested) and removed 27 (18 requested) atoms. Cycle 7: After refmac, R = 0.2993 (Rfree = 0.000) for 2001 atoms. Found 32 (36 requested) and removed 20 (18 requested) atoms. Cycle 8: After refmac, R = 0.2876 (Rfree = 0.000) for 2003 atoms. Found 19 (36 requested) and removed 22 (18 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2754 (Rfree = 0.000) for 1993 atoms. Found 24 (36 requested) and removed 19 (18 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2628 (Rfree = 0.000) for 1990 atoms. Found 14 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.68 2.12 Round 1: 156 peptides, 20 chains. Longest chain 20 peptides. Score 0.485 Round 2: 165 peptides, 20 chains. Longest chain 35 peptides. Score 0.515 Round 3: 157 peptides, 20 chains. Longest chain 20 peptides. Score 0.488 Round 4: 166 peptides, 21 chains. Longest chain 22 peptides. Score 0.503 Round 5: 165 peptides, 20 chains. Longest chain 24 peptides. Score 0.515 Taking the results from Round 5 Chains 21, Residues 145, Estimated correctness of the model 61.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 15130 reflections ( 99.41 % complete ) and 4098 restraints for refining 2023 atoms. 3510 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2909 (Rfree = 0.000) for 2023 atoms. Found 35 (36 requested) and removed 23 (18 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2776 (Rfree = 0.000) for 2029 atoms. Found 30 (36 requested) and removed 18 (18 requested) atoms. Cycle 13: After refmac, R = 0.2721 (Rfree = 0.000) for 2034 atoms. Found 31 (36 requested) and removed 19 (18 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2617 (Rfree = 0.000) for 2041 atoms. Found 16 (37 requested) and removed 19 (18 requested) atoms. Cycle 15: After refmac, R = 0.2578 (Rfree = 0.000) for 2031 atoms. Found 21 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.66 2.10 Round 1: 158 peptides, 22 chains. Longest chain 23 peptides. Score 0.460 Round 2: 168 peptides, 18 chains. Longest chain 24 peptides. Score 0.554 Round 3: 163 peptides, 18 chains. Longest chain 27 peptides. Score 0.538 Round 4: 168 peptides, 21 chains. Longest chain 23 peptides. Score 0.509 Round 5: 173 peptides, 21 chains. Longest chain 17 peptides. Score 0.526 Taking the results from Round 2 Chains 22, Residues 150, Estimated correctness of the model 67.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 15130 reflections ( 99.41 % complete ) and 3848 restraints for refining 2024 atoms. 3177 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2797 (Rfree = 0.000) for 2024 atoms. Found 36 (36 requested) and removed 23 (18 requested) atoms. Cycle 17: After refmac, R = 0.2647 (Rfree = 0.000) for 2035 atoms. Found 16 (36 requested) and removed 19 (18 requested) atoms. Cycle 18: After refmac, R = 0.2562 (Rfree = 0.000) for 2025 atoms. Found 18 (36 requested) and removed 18 (18 requested) atoms. Cycle 19: After refmac, R = 0.2540 (Rfree = 0.000) for 2018 atoms. Found 21 (36 requested) and removed 18 (18 requested) atoms. Cycle 20: After refmac, R = 0.2514 (Rfree = 0.000) for 2019 atoms. Found 19 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.69 2.12 Round 1: 158 peptides, 22 chains. Longest chain 17 peptides. Score 0.460 Round 2: 168 peptides, 20 chains. Longest chain 17 peptides. Score 0.524 Round 3: 171 peptides, 20 chains. Longest chain 21 peptides. Score 0.534 Round 4: 162 peptides, 16 chains. Longest chain 19 peptides. Score 0.565 Round 5: 171 peptides, 20 chains. Longest chain 24 peptides. Score 0.534 Taking the results from Round 4 Chains 17, Residues 146, Estimated correctness of the model 68.5 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 15130 reflections ( 99.41 % complete ) and 3927 restraints for refining 2023 atoms. 3317 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2720 (Rfree = 0.000) for 2023 atoms. Found 33 (36 requested) and removed 19 (18 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2595 (Rfree = 0.000) for 2028 atoms. Found 19 (36 requested) and removed 18 (18 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2546 (Rfree = 0.000) for 2024 atoms. Found 20 (36 requested) and removed 18 (18 requested) atoms. Cycle 24: After refmac, R = 0.2509 (Rfree = 0.000) for 2025 atoms. Found 11 (36 requested) and removed 18 (18 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2476 (Rfree = 0.000) for 2012 atoms. Found 18 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.69 2.12 Round 1: 150 peptides, 19 chains. Longest chain 15 peptides. Score 0.480 Round 2: 160 peptides, 16 chains. Longest chain 20 peptides. Score 0.558 Round 3: 160 peptides, 14 chains. Longest chain 35 peptides. Score 0.588 Round 4: 164 peptides, 16 chains. Longest chain 25 peptides. Score 0.571 Round 5: 165 peptides, 20 chains. Longest chain 23 peptides. Score 0.515 Taking the results from Round 3 Chains 15, Residues 146, Estimated correctness of the model 71.5 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 15130 reflections ( 99.41 % complete ) and 3801 restraints for refining 2024 atoms. 3135 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2726 (Rfree = 0.000) for 2024 atoms. Found 31 (36 requested) and removed 18 (18 requested) atoms. Cycle 27: After refmac, R = 0.2618 (Rfree = 0.000) for 2033 atoms. Found 15 (36 requested) and removed 18 (18 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2562 (Rfree = 0.000) for 2027 atoms. Found 19 (36 requested) and removed 18 (18 requested) atoms. Cycle 29: After refmac, R = 0.2590 (Rfree = 0.000) for 2027 atoms. Found 16 (36 requested) and removed 19 (18 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2500 (Rfree = 0.000) for 2023 atoms. Found 20 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.68 2.12 Round 1: 158 peptides, 20 chains. Longest chain 20 peptides. Score 0.492 Round 2: 167 peptides, 19 chains. Longest chain 20 peptides. Score 0.536 Round 3: 166 peptides, 20 chains. Longest chain 22 peptides. Score 0.518 Round 4: 173 peptides, 18 chains. Longest chain 23 peptides. Score 0.569 Round 5: 163 peptides, 20 chains. Longest chain 26 peptides. Score 0.508 Taking the results from Round 4 Chains 19, Residues 155, Estimated correctness of the model 69.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 15130 reflections ( 99.41 % complete ) and 3881 restraints for refining 2024 atoms. 3251 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2689 (Rfree = 0.000) for 2024 atoms. Found 36 (36 requested) and removed 20 (18 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2598 (Rfree = 0.000) for 2039 atoms. Found 22 (36 requested) and removed 18 (18 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2530 (Rfree = 0.000) for 2041 atoms. Found 22 (37 requested) and removed 18 (18 requested) atoms. Cycle 34: After refmac, R = 0.2518 (Rfree = 0.000) for 2040 atoms. Found 18 (37 requested) and removed 19 (18 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2473 (Rfree = 0.000) for 2036 atoms. Found 15 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.67 2.11 Round 1: 155 peptides, 22 chains. Longest chain 14 peptides. Score 0.450 Round 2: 162 peptides, 18 chains. Longest chain 19 peptides. Score 0.535 Round 3: 159 peptides, 19 chains. Longest chain 35 peptides. Score 0.510 Round 4: 159 peptides, 19 chains. Longest chain 23 peptides. Score 0.510 Round 5: 164 peptides, 22 chains. Longest chain 19 peptides. Score 0.481 Taking the results from Round 2 Chains 18, Residues 144, Estimated correctness of the model 64.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15130 reflections ( 99.41 % complete ) and 4064 restraints for refining 2023 atoms. 3506 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2746 (Rfree = 0.000) for 2023 atoms. Found 31 (36 requested) and removed 19 (18 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2631 (Rfree = 0.000) for 2033 atoms. Found 23 (36 requested) and removed 18 (18 requested) atoms. Cycle 38: After refmac, R = 0.2613 (Rfree = 0.000) for 2036 atoms. Found 30 (36 requested) and removed 18 (18 requested) atoms. Cycle 39: After refmac, R = 0.2460 (Rfree = 0.000) for 2047 atoms. Found 19 (37 requested) and removed 18 (18 requested) atoms. Cycle 40: After refmac, R = 0.2462 (Rfree = 0.000) for 2047 atoms. Found 15 (37 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.65 2.09 Round 1: 149 peptides, 21 chains. Longest chain 18 peptides. Score 0.444 Round 2: 162 peptides, 19 chains. Longest chain 22 peptides. Score 0.520 Round 3: 169 peptides, 21 chains. Longest chain 18 peptides. Score 0.513 Round 4: 168 peptides, 19 chains. Longest chain 19 peptides. Score 0.539 Round 5: 162 peptides, 20 chains. Longest chain 23 peptides. Score 0.505 Taking the results from Round 4 Chains 20, Residues 149, Estimated correctness of the model 65.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 15130 reflections ( 99.41 % complete ) and 3926 restraints for refining 2024 atoms. 3324 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2738 (Rfree = 0.000) for 2024 atoms. Found 36 (36 requested) and removed 20 (18 requested) atoms. Cycle 42: After refmac, R = 0.2574 (Rfree = 0.000) for 2038 atoms. Found 24 (36 requested) and removed 18 (18 requested) atoms. Cycle 43: After refmac, R = 0.2515 (Rfree = 0.000) for 2043 atoms. Found 12 (37 requested) and removed 18 (18 requested) atoms. Cycle 44: After refmac, R = 0.2451 (Rfree = 0.000) for 2034 atoms. Found 11 (36 requested) and removed 18 (18 requested) atoms. Cycle 45: After refmac, R = 0.2461 (Rfree = 0.000) for 2023 atoms. Found 19 (36 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.70 2.13 Round 1: 149 peptides, 24 chains. Longest chain 10 peptides. Score 0.395 Round 2: 158 peptides, 20 chains. Longest chain 18 peptides. Score 0.492 Round 3: 167 peptides, 20 chains. Longest chain 18 peptides. Score 0.521 Round 4: 159 peptides, 20 chains. Longest chain 19 peptides. Score 0.495 Round 5: 159 peptides, 19 chains. Longest chain 34 peptides. Score 0.510 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 147, Estimated correctness of the model 62.4 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2p4g-2_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15130 reflections ( 99.41 % complete ) and 4074 restraints for refining 2024 atoms. 3506 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2642 (Rfree = 0.000) for 2024 atoms. Found 0 (36 requested) and removed 7 (18 requested) atoms. Cycle 47: After refmac, R = 0.2574 (Rfree = 0.000) for 2015 atoms. Found 0 (36 requested) and removed 5 (18 requested) atoms. Cycle 48: After refmac, R = 0.2573 (Rfree = 0.000) for 2008 atoms. Found 0 (36 requested) and removed 5 (18 requested) atoms. Cycle 49: After refmac, R = 0.2569 (Rfree = 0.000) for 2002 atoms. Found 0 (36 requested) and removed 4 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:17:14 GMT 2018 Job finished. TimeTaking 49.27