null Sun 23 Dec 22:22:52 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 2pn1-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pn1-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pn1-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-2.0-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/2pn1-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-2.0-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 22:23:01 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/2pn1-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-2.0-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 319 and 0 Target number of residues in the AU: 319 Target solvent content: 0.5147 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 331 Adjusted target solvent content: 0.50 Input MTZ file: 2pn1-2.0-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: 5 Cell parameters: 91.460 61.130 76.770 90.000 124.022 90.000 Input sequence file: 2pn1-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2648 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 1 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: 63.629 2.000 Wilson plot Bfac: 26.45 23352 reflections ( 97.81 % complete ) and 0 restraints for refining 2931 atoms. Observations/parameters ratio is 1.99 ------------------------------------------------------ Starting model: R = 0.3706 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3224 (Rfree = 0.000) for 2931 atoms. Found 54 (100 requested) and removed 63 (50 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.17 2.17 Round 1: 146 peptides, 29 chains. Longest chain 13 peptides. Score 0.320 Round 2: 155 peptides, 26 chains. Longest chain 12 peptides. Score 0.421 Round 3: 158 peptides, 24 chains. Longest chain 18 peptides. Score 0.471 Round 4: 182 peptides, 25 chains. Longest chain 24 peptides. Score 0.547 Round 5: 178 peptides, 24 chains. Longest chain 21 peptides. Score 0.549 Taking the results from Round 5 Chains 24, Residues 154, Estimated correctness of the model 83.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 23352 reflections ( 97.81 % complete ) and 5490 restraints for refining 2568 atoms. 4898 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3505 (Rfree = 0.000) for 2568 atoms. Found 66 (87 requested) and removed 47 (43 requested) atoms. Cycle 2: After refmac, R = 0.3251 (Rfree = 0.000) for 2576 atoms. Found 43 (88 requested) and removed 44 (44 requested) atoms. Cycle 3: After refmac, R = 0.3060 (Rfree = 0.000) for 2571 atoms. Found 42 (88 requested) and removed 32 (44 requested) atoms. Cycle 4: After refmac, R = 0.2910 (Rfree = 0.000) for 2573 atoms. Found 33 (88 requested) and removed 23 (44 requested) atoms. Cycle 5: After refmac, R = 0.2845 (Rfree = 0.000) for 2579 atoms. Found 24 (88 requested) and removed 12 (44 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.12 2.12 Round 1: 175 peptides, 28 chains. Longest chain 17 peptides. Score 0.469 Round 2: 174 peptides, 24 chains. Longest chain 22 peptides. Score 0.534 Round 3: 180 peptides, 26 chains. Longest chain 19 peptides. Score 0.523 Round 4: 176 peptides, 22 chains. Longest chain 22 peptides. Score 0.574 Round 5: 181 peptides, 24 chains. Longest chain 24 peptides. Score 0.560 Taking the results from Round 4 Chains 22, Residues 154, Estimated correctness of the model 85.1 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 23352 reflections ( 97.81 % complete ) and 5488 restraints for refining 2568 atoms. 4861 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3067 (Rfree = 0.000) for 2568 atoms. Found 74 (87 requested) and removed 38 (43 requested) atoms. Cycle 7: After refmac, R = 0.2869 (Rfree = 0.000) for 2603 atoms. Found 35 (89 requested) and removed 16 (44 requested) atoms. Cycle 8: After refmac, R = 0.2739 (Rfree = 0.000) for 2620 atoms. Found 36 (89 requested) and removed 16 (44 requested) atoms. Cycle 9: After refmac, R = 0.2679 (Rfree = 0.000) for 2639 atoms. Found 24 (90 requested) and removed 8 (45 requested) atoms. Cycle 10: After refmac, R = 0.2621 (Rfree = 0.000) for 2655 atoms. Found 22 (90 requested) and removed 5 (45 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.09 2.09 Round 1: 172 peptides, 27 chains. Longest chain 17 peptides. Score 0.474 Round 2: 185 peptides, 23 chains. Longest chain 22 peptides. Score 0.590 Round 3: 199 peptides, 25 chains. Longest chain 22 peptides. Score 0.607 Round 4: 191 peptides, 22 chains. Longest chain 22 peptides. Score 0.625 Round 5: 192 peptides, 22 chains. Longest chain 22 peptides. Score 0.628 Taking the results from Round 5 Chains 24, Residues 170, Estimated correctness of the model 88.4 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 23352 reflections ( 97.81 % complete ) and 4995 restraints for refining 2568 atoms. 4288 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2936 (Rfree = 0.000) for 2568 atoms. Found 64 (87 requested) and removed 28 (43 requested) atoms. Cycle 12: After refmac, R = 0.2745 (Rfree = 0.000) for 2600 atoms. Found 44 (89 requested) and removed 7 (44 requested) atoms. Cycle 13: After refmac, R = 0.2654 (Rfree = 0.000) for 2636 atoms. Found 23 (90 requested) and removed 8 (45 requested) atoms. Cycle 14: After refmac, R = 0.2579 (Rfree = 0.000) for 2651 atoms. Found 15 (90 requested) and removed 6 (45 requested) atoms. Cycle 15: After refmac, R = 0.2531 (Rfree = 0.000) for 2658 atoms. Found 14 (91 requested) and removed 7 (45 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.09 2.09 Round 1: 186 peptides, 26 chains. Longest chain 22 peptides. Score 0.546 Round 2: 187 peptides, 23 chains. Longest chain 21 peptides. Score 0.597 Round 3: 200 peptides, 25 chains. Longest chain 19 peptides. Score 0.610 Round 4: 202 peptides, 22 chains. Longest chain 25 peptides. Score 0.659 Round 5: 195 peptides, 24 chains. Longest chain 17 peptides. Score 0.608 Taking the results from Round 4 Chains 24, Residues 180, Estimated correctness of the model 90.1 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 23352 reflections ( 97.81 % complete ) and 4954 restraints for refining 2626 atoms. 4161 conditional restraints added. Observations/parameters ratio is 2.22 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2844 (Rfree = 0.000) for 2626 atoms. Found 80 (89 requested) and removed 40 (44 requested) atoms. Cycle 17: After refmac, R = 0.2670 (Rfree = 0.000) for 2665 atoms. Found 43 (91 requested) and removed 14 (45 requested) atoms. Cycle 18: After refmac, R = 0.2547 (Rfree = 0.000) for 2692 atoms. Found 44 (92 requested) and removed 7 (46 requested) atoms. Cycle 19: After refmac, R = 0.2477 (Rfree = 0.000) for 2727 atoms. Found 27 (93 requested) and removed 7 (46 requested) atoms. Cycle 20: After refmac, R = 0.2419 (Rfree = 0.000) for 2747 atoms. Found 23 (94 requested) and removed 3 (47 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.08 2.08 Round 1: 196 peptides, 26 chains. Longest chain 18 peptides. Score 0.582 Round 2: 210 peptides, 22 chains. Longest chain 25 peptides. Score 0.682 Round 3: 197 peptides, 21 chains. Longest chain 21 peptides. Score 0.658 Round 4: 203 peptides, 21 chains. Longest chain 34 peptides. Score 0.675 Round 5: 197 peptides, 21 chains. Longest chain 31 peptides. Score 0.658 Taking the results from Round 2 Chains 26, Residues 188, Estimated correctness of the model 91.3 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 23352 reflections ( 97.81 % complete ) and 5024 restraints for refining 2714 atoms. 4159 conditional restraints added. Observations/parameters ratio is 2.15 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2664 (Rfree = 0.000) for 2714 atoms. Found 76 (92 requested) and removed 33 (46 requested) atoms. Cycle 22: After refmac, R = 0.2528 (Rfree = 0.000) for 2756 atoms. Found 37 (94 requested) and removed 8 (47 requested) atoms. Cycle 23: After refmac, R = 0.2462 (Rfree = 0.000) for 2782 atoms. Found 28 (95 requested) and removed 4 (47 requested) atoms. Cycle 24: After refmac, R = 0.2416 (Rfree = 0.000) for 2802 atoms. Found 31 (96 requested) and removed 7 (48 requested) atoms. Cycle 25: After refmac, R = 0.2363 (Rfree = 0.000) for 2825 atoms. Found 20 (96 requested) and removed 7 (48 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.09 2.09 Round 1: 195 peptides, 24 chains. Longest chain 17 peptides. Score 0.608 Round 2: 199 peptides, 18 chains. Longest chain 37 peptides. Score 0.703 Round 3: 193 peptides, 21 chains. Longest chain 17 peptides. Score 0.646 Round 4: 194 peptides, 19 chains. Longest chain 37 peptides. Score 0.676 Round 5: 192 peptides, 21 chains. Longest chain 31 peptides. Score 0.643 Taking the results from Round 2 Chains 18, Residues 181, Estimated correctness of the model 92.3 % 2 chains (41 residues) have been docked in sequence Building loops using Loopy2018 18 chains (181 residues) following loop building 2 chains (41 residues) in sequence following loop building ------------------------------------------------------ 23352 reflections ( 97.81 % complete ) and 5116 restraints for refining 2769 atoms. 4241 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2579 (Rfree = 0.000) for 2769 atoms. Found 88 (94 requested) and removed 37 (47 requested) atoms. Cycle 27: After refmac, R = 0.2429 (Rfree = 0.000) for 2819 atoms. Found 47 (96 requested) and removed 11 (48 requested) atoms. Cycle 28: After refmac, R = 0.2331 (Rfree = 0.000) for 2854 atoms. Found 46 (97 requested) and removed 10 (48 requested) atoms. Cycle 29: After refmac, R = 0.2254 (Rfree = 0.000) for 2887 atoms. Found 34 (98 requested) and removed 8 (49 requested) atoms. Cycle 30: After refmac, R = 0.2235 (Rfree = 0.000) for 2911 atoms. Found 33 (99 requested) and removed 5 (49 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.07 2.07 Round 1: 180 peptides, 22 chains. Longest chain 23 peptides. Score 0.588 Round 2: 189 peptides, 19 chains. Longest chain 31 peptides. Score 0.662 Round 3: 188 peptides, 19 chains. Longest chain 25 peptides. Score 0.659 Round 4: 181 peptides, 19 chains. Longest chain 31 peptides. Score 0.637 Round 5: 179 peptides, 19 chains. Longest chain 25 peptides. Score 0.631 Taking the results from Round 2 Chains 19, Residues 170, Estimated correctness of the model 90.3 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 23352 reflections ( 97.81 % complete ) and 5269 restraints for refining 2843 atoms. 4453 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2405 (Rfree = 0.000) for 2843 atoms. Found 92 (97 requested) and removed 39 (48 requested) atoms. Cycle 32: After refmac, R = 0.2308 (Rfree = 0.000) for 2895 atoms. Found 49 (99 requested) and removed 8 (49 requested) atoms. Cycle 33: After refmac, R = 0.2222 (Rfree = 0.000) for 2931 atoms. Found 37 (100 requested) and removed 12 (50 requested) atoms. Cycle 34: After refmac, R = 0.2211 (Rfree = 0.000) for 2954 atoms. Found 30 (101 requested) and removed 14 (50 requested) atoms. Cycle 35: After refmac, R = 0.2162 (Rfree = 0.000) for 2969 atoms. Found 25 (101 requested) and removed 7 (50 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.07 2.07 Round 1: 192 peptides, 19 chains. Longest chain 37 peptides. Score 0.671 Round 2: 195 peptides, 20 chains. Longest chain 25 peptides. Score 0.666 Round 3: 190 peptides, 18 chains. Longest chain 37 peptides. Score 0.678 Round 4: 190 peptides, 18 chains. Longest chain 20 peptides. Score 0.678 Round 5: 185 peptides, 19 chains. Longest chain 37 peptides. Score 0.650 Taking the results from Round 4 Chains 18, Residues 172, Estimated correctness of the model 91.1 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 23352 reflections ( 97.81 % complete ) and 5565 restraints for refining 2872 atoms. 4836 conditional restraints added. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2386 (Rfree = 0.000) for 2872 atoms. Found 85 (98 requested) and removed 22 (49 requested) atoms. Cycle 37: After refmac, R = 0.2249 (Rfree = 0.000) for 2932 atoms. Found 48 (100 requested) and removed 6 (50 requested) atoms. Cycle 38: After refmac, R = 0.2183 (Rfree = 0.000) for 2973 atoms. Found 30 (101 requested) and removed 8 (50 requested) atoms. Cycle 39: After refmac, R = 0.2134 (Rfree = 0.000) for 2995 atoms. Found 35 (102 requested) and removed 12 (51 requested) atoms. Cycle 40: After refmac, R = 0.2115 (Rfree = 0.000) for 3018 atoms. Found 35 (103 requested) and removed 11 (51 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.07 2.07 Round 1: 192 peptides, 22 chains. Longest chain 20 peptides. Score 0.628 Round 2: 202 peptides, 21 chains. Longest chain 23 peptides. Score 0.672 Round 3: 204 peptides, 22 chains. Longest chain 38 peptides. Score 0.665 Round 4: 202 peptides, 21 chains. Longest chain 22 peptides. Score 0.672 Round 5: 196 peptides, 20 chains. Longest chain 25 peptides. Score 0.669 Taking the results from Round 4 Chains 21, Residues 181, Estimated correctness of the model 90.8 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 23352 reflections ( 97.81 % complete ) and 5653 restraints for refining 2932 atoms. 4860 conditional restraints added. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2371 (Rfree = 0.000) for 2932 atoms. Found 87 (100 requested) and removed 23 (50 requested) atoms. Cycle 42: After refmac, R = 0.2220 (Rfree = 0.000) for 2996 atoms. Found 60 (102 requested) and removed 6 (51 requested) atoms. Cycle 43: After refmac, R = 0.2144 (Rfree = 0.000) for 3050 atoms. Found 36 (104 requested) and removed 5 (52 requested) atoms. Cycle 44: After refmac, R = 0.2095 (Rfree = 0.000) for 3080 atoms. Found 48 (105 requested) and removed 5 (52 requested) atoms. Cycle 45: After refmac, R = 0.2044 (Rfree = 0.000) for 3120 atoms. Found 35 (106 requested) and removed 10 (53 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.06 2.06 Round 1: 203 peptides, 20 chains. Longest chain 25 peptides. Score 0.688 Round 2: 202 peptides, 18 chains. Longest chain 41 peptides. Score 0.711 Round 3: 194 peptides, 18 chains. Longest chain 25 peptides. Score 0.690 Round 4: 194 peptides, 22 chains. Longest chain 21 peptides. Score 0.635 Round 5: 199 peptides, 20 chains. Longest chain 32 peptides. Score 0.677 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 184, Estimated correctness of the model 92.7 % 4 chains (53 residues) have been docked in sequence Sequence coverage is 28 % Consider running further cycles of model building using 2pn1-2_warpNtrace.pdb as input Building loops using Loopy2018 23 chains (184 residues) following loop building 4 chains (53 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 23352 reflections ( 97.81 % complete ) and 5622 restraints for refining 3083 atoms. 4678 conditional restraints added. Observations/parameters ratio is 1.89 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2327 (Rfree = 0.000) for 3083 atoms. Found 0 (105 requested) and removed 9 (52 requested) atoms. Cycle 47: After refmac, R = 0.2247 (Rfree = 0.000) for 3072 atoms. Found 0 (103 requested) and removed 4 (52 requested) atoms. Cycle 48: After refmac, R = 0.2214 (Rfree = 0.000) for 3067 atoms. Found 0 (101 requested) and removed 2 (52 requested) atoms. Cycle 49: After refmac, R = 0.2190 (Rfree = 0.000) for 3065 atoms. Found 0 (99 requested) and removed 1 (52 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:14:17 GMT 2018 Job finished. TimeTaking 51.41 Used memory is bytes: 5870448